subject:"\[ccp4bb\] Unusual dataset with high Rmerge and extremely low b\-factors\?"

[ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

2019-11-03 Thread Michael Jarva

Hi CCP4BB,

I have some unusual crystal diffraction data I'd like to get your input on.

Almost a year ago I shot some small rods sticking out of a loop, so basically 
no liquid around them - using the microfocus MX2 beamline at the australian 
synchrotron, collected on an EIGER 16M detector.

The crystals diffracted weakly and was seemingly not viable at first glance 
because of high Rmerge/Rpims. See the aimless summary at the bottom of this 
post. This seemed to stem from a low spot intensity at low resolutions 
(I/sd(I)=4.6), but since the CC1/2 was fine I went with it anyway.

Here I also noted an unusually low Mosaicity, 0.05, and Wilson B-factors, 8.02 
Å^2.

Density maps looked great and the build refined easily enough (R/Rfree 
0.1939/0.2259) with a mean B-factor of 19.85, which according to phenix is 
lower than any other structure deposited in that resolution bin. Furthermore, 
the molprobity score is 0.83, and overall real-space correlation CC is 0.855.

So my question is, can I feel comfortable depositing this?

best regards
Michael

Chosen Solution:space group P 1 21 1
Unit cell:44.93   41.90   45.83  90.00  115.57   90.00
Number of batches in file:   1659
The data do not appear to be twinned, from the L-test
Overall InnerShell OuterShell

Low resolution limit   41.34 41.34  2.49

High resolution limit   2.40  8.98  2.40


Rmerge  (within I+/I-) 0.231 0.084 0.782

Rmerge  (all I+ and I-)0.266 0.099 0.983

Rmeas (within I+/I-)   0.323 0.118 1.091

Rmeas (all I+ & I-)0.317 0.118 1.167

Rpim (within I+/I-)0.225 0.084 0.759

Rpim (all I+ & I-) 0.171 0.063 0.623

Rmerge in top intensity bin0.079- -

Total number of observations   19901   362  2067

Total number unique 6054   126   611

Mean((I)/sd(I))  2.7   4.6   1.0

Mn(I) half-set correlation CC(1/2) 0.958 0.991 0.570

Completeness98.6  98.2  97.3

Multiplicity 3.3   2.9   3.4

Mean(Chi^2) 0.48  0.33  0.50


Anomalous completeness  81.7  92.2  75.1

Anomalous multiplicity   1.5   1.8   1.9

DelAnom correlation between half-sets -0.003 0.041 0.045

Mid-Slope of Anom Normal Probability   0.704   - -


The anomalous signal appears to be weak so anomalous flag was left OFF


Estimates of resolution limits: overall

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.67A

   from Mn(I/sd) >  2.00: limit =  2.87A


Estimates of resolution limits in reciprocal lattice directions:

  Along0.96 a* - 0.28 c*

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.40A  == maximum 
resolution

  Along k axis

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.86A

  Along   -0.17 a* + 0.99 c*

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.98A


Anisotropic deltaB (i.e. range of principal components), A^2:  8.62


Average unit cell:44.93   41.90   45.83   90.00  115.57   90.00

Space group: P 1 21 1

Average mosaicity:   0.05


Minimum and maximum SD correction factors: Fulls   1.27   1.28 Partials   0.00  
 0.00





Michael Jarva, PhD
ACRF Chemical Biology Division

The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade
Parkville Victoria 3052
Australia

Phone: +61 3 9345 2493
Email: jarv...@wehi.edu.au | Web: http://www.wehi.edu.au/

The ACRF Chemical Biology Division is supported by the

Australian Cancer Research Foundation


___

The information in this email is confidential and intended solely for the 
addressee.
You must not disclose, forward, print or use it without the permission of the 
sender.

The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the 
Kulin
Nation as the traditional owners of the land where our campuses are located and
the continuing connection to country and community.
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Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

2019-11-03 Thread Jon Cooper

Given that the I/sigma(I) is quite low the high R-merge values are probably to be expected. If the data were stronger, an R-merge that high would indicate that the space group was wrong or the data misindexed. If the multiplicity was higher you could process the data in lower symmetry space group (P1) and see if the R-merge became appreciably lower, but I'm not sure that it will be sensible to do that with such a low multiplicity, still it's probably worth doing. I think if you explain the vagaries of the crystals and data when you publish and/or deposit, I think it should be OK with the referees, especially if the map looks good. I would not worry too much about the mean B-factor but it might be interesting to see the Wilson plot.On 3 Nov 2019 23:18, Michael Jarva  wrote:

Hi CCP4BB,




I have some unusual crystal diffraction data I'd like to get your input on.




Almost a year ago I shot some small rods sticking out of a loop, so basically no liquid around them - using the microfocus MX2 beamline at the australian synchrotron, collected on an EIGER 16M detector.




The crystals diffracted weakly and was seemingly not viable at first glance because of high Rmerge/Rpims. See the aimless summary at the bottom of this post. This seemed to stem from a low spot intensity at low resolutions (I/sd(I)=4.6), but since the CC1/2
 was fine I went with it anyway.




Here I also noted an unusually low Mosaicity, 0.05, and Wilson B-factors, 8.02 Å^2.




Density maps looked great and the build refined easily enough (R/Rfree 0.1939/0.2259) with a mean B-factor of 19.85, which according to phenix is lower than any other structure deposited in that resolution bin. Furthermore, the
 molprobity score is 0.83, and overall real-space correlation CC is 0.855.




So my question is, can I feel comfortable depositing this? 




best regards

Michael





Chosen Solution:    space group P 1 21 1

Unit cell:    44.93   41.90   45.83      90.00  115.57   90.00

Number of batches in file:   1659

The data do not appear to be twinned, from the L-test



Overall InnerShell OuterShell



Low resolution limit   41.34 41.34  2.49
High resolution limit   2.40  8.98  2.40

Rmerge  (within I+/I-) 0.231 0.084 0.782
Rmerge  (all I+ and I-)0.266 0.099 0.983
Rmeas (within I+/I-)   0.323 0.118 1.091
Rmeas (all I+ & I-)0.317 0.118 1.167
Rpim (within I+/I-)0.225 0.084 0.759
Rpim (all I+ & I-) 0.171 0.063 0.623
Rmerge in top intensity bin0.079- - 
Total number of observations   19901   362  2067
Total number unique 6054   126   611
Mean((I)/sd(I))  2.7   4.6   1.0
Mn(I) half-set correlation CC(1/2) 0.958 0.991 0.570
Completeness98.6  98.2  97.3
Multiplicity 3.3   2.9   3.4
Mean(Chi^2) 0.48  0.33  0.50

Anomalous completeness  81.7  92.2  75.1
Anomalous multiplicity   1.5   1.8   1.9
DelAnom correlation between half-sets -0.003 0.041 0.045
Mid-Slope of Anom Normal Probability   0.704   - -  

The anomalous signal appears to be weak so anomalous flag was left OFF

Estimates of resolution limits: overall
   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum resolution
   from Mn(I/sd) >  1.50: limit =  2.67A 
   from Mn(I/sd) >  2.00: limit =  2.87A 

Estimates of resolution limits in reciprocal lattice directions:
  Along0.96 a* - 0.28 c*
   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum resolution
   from Mn(I/sd) >  1.50: limit =  2.40A  == maximum resolution
  Along k axis
   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum resolution
   from Mn(I/sd) >  1.50: limit =  2.86A 
  Along   -0.17 a* + 0.99 c*
   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum resolution
   from Mn(I/sd) >  1.50: limit =  2.98A 

Anisotropic deltaB (i.e. range of principal components), A^2:  8.62

Average unit cell:44.93   41.90   45.83   90.00  115.57   90.00
Space group: P 1 21 1
Average mosaicity:   0.05

Minimum and maximum SD correction factors: Fulls   1.27   1.28 Partials   0.00   0.00















Michael Jarva, PhD
ACRF Chemical Biology Division

The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade
Parkville Victoria 3052
Australia

Phone: +61 3 9345 2493 
Email: jarv...@wehi.edu.au | Web: http://www.wehi.edu.au/

The ACRF Chemical Biology Divisio

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

2019-11-03 Thread Anastassis Perrakis

Dear Michael,

Exactly because the B factor is only 8, the intensity as function of resolution 
is droping really slowly, and thus the I/sigI 4.7 at low resolution drops so 
slowly to 1.0.

I would almost bet you have a low solvent content.

The data are fine imo.

Best,

Tassos

On Nov 4, 2019, at 0:18, Michael Jarva 
mailto:jarv...@wehi.edu.au>> wrote:

Hi CCP4BB,

I have some unusual crystal diffraction data I'd like to get your input on.

Almost a year ago I shot some small rods sticking out of a loop, so basically 
no liquid around them - using the microfocus MX2 beamline at the australian 
synchrotron, collected on an EIGER 16M detector.

The crystals diffracted weakly and was seemingly not viable at first glance 
because of high Rmerge/Rpims. See the aimless summary at the bottom of this 
post. This seemed to stem from a low spot intensity at low resolutions 
(I/sd(I)=4.6), but since the CC1/2 was fine I went with it anyway.

Here I also noted an unusually low Mosaicity, 0.05, and Wilson B-factors, 8.02 
Å^2.

Density maps looked great and the build refined easily enough (R/Rfree 
0.1939/0.2259) with a mean B-factor of 19.85, which according to phenix is 
lower than any other structure deposited in that resolution bin. Furthermore, 
the molprobity score is 0.83, and overall real-space correlation CC is 0.855.

So my question is, can I feel comfortable depositing this?

best regards
Michael

Chosen Solution:space group P 1 21 1
Unit cell:44.93   41.90   45.83  90.00  115.57   90.00
Number of batches in file:   1659
The data do not appear to be twinned, from the L-test
Overall InnerShell OuterShell

Low resolution limit   41.34 41.34  2.49

High resolution limit   2.40  8.98  2.40


Rmerge  (within I+/I-) 0.231 0.084 0.782

Rmerge  (all I+ and I-)0.266 0.099 0.983

Rmeas (within I+/I-)   0.323 0.118 1.091

Rmeas (all I+ & I-)0.317 0.118 1.167

Rpim (within I+/I-)0.225 0.084 0.759

Rpim (all I+ & I-) 0.171 0.063 0.623

Rmerge in top intensity bin0.079- -

Total number of observations   19901   362  2067

Total number unique 6054   126   611

Mean((I)/sd(I))  2.7   4.6   1.0

Mn(I) half-set correlation CC(1/2) 0.958 0.991 0.570

Completeness98.6  98.2  97.3

Multiplicity 3.3   2.9   3.4

Mean(Chi^2) 0.48  0.33  0.50


Anomalous completeness  81.7  92.2  75.1

Anomalous multiplicity   1.5   1.8   1.9

DelAnom correlation between half-sets -0.003 0.041 0.045

Mid-Slope of Anom Normal Probability   0.704   - -


The anomalous signal appears to be weak so anomalous flag was left OFF


Estimates of resolution limits: overall

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.67A

   from Mn(I/sd) >  2.00: limit =  2.87A


Estimates of resolution limits in reciprocal lattice directions:

  Along0.96 a* - 0.28 c*

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.40A  == maximum 
resolution

  Along k axis

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.86A

  Along   -0.17 a* + 0.99 c*

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.98A


Anisotropic deltaB (i.e. range of principal components), A^2:  8.62


Average unit cell:44.93   41.90   45.83   90.00  115.57   90.00

Space group: P 1 21 1

Average mosaicity:   0.05


Minimum and maximum SD correction factors: Fulls   1.27   1.28 Partials   0.00  
 0.00





Michael Jarva, PhD
ACRF Chemical Biology Division
The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade
Parkville Victoria 3052
Australia
Phone: +61 3 9345 2493
Email: jarv...@wehi.edu.au | Web: 
http://www.wehi.edu.au/
The ACRF Chemical Biology Division is supported by the
Australian Cancer Research Foundation


___

The information in this email is confidential and intended solely for the 
addressee.
You must not disclose, forward, print or use it without the permission of the 
sender.

The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the 
Kulin
Nation as the traditional owners

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

2019-11-04 Thread Eleanor Dodson

My first check would be to inspect the data processing plots -
Wilson Plot? Is it normal? predicted B factor of 8 - why?

Then the plot from  refmac  and  v resolution?
Is there a scaling abnormality?

B of 8 is surprisingly low for that resolution  but maybe the crystals just
did not have enough oomph to go to their limit..

Eleanor




On Mon, 4 Nov 2019 at 07:00, Anastassis Perrakis  wrote:

> Dear Michael,
>
> Exactly because the B factor is only 8, the intensity as function of
> resolution is droping really slowly, and thus the I/sigI 4.7 at low
> resolution drops so slowly to 1.0.
>
> I would almost bet you have a low solvent content.
>
> The data are fine imo.
>
> Best,
>
> Tassos
>
> On Nov 4, 2019, at 0:18, Michael Jarva  wrote:
>
> Hi CCP4BB,
>
> I have some unusual crystal diffraction data I'd like to get your input on.
>
> Almost a year ago I shot some small rods sticking out of a loop, so
> basically no liquid around them - using the microfocus MX2 beamline at the
> australian synchrotron, collected on an EIGER 16M detector.
>
> The crystals diffracted weakly and was seemingly not viable at first
> glance because of high Rmerge/Rpims. See the aimless summary at the bottom
> of this post. This seemed to stem from a low spot intensity at low
> resolutions (I/sd(I)=4.6), but since the CC1/2 was fine I went with it
> anyway.
>
> Here I also noted an unusually low Mosaicity, 0.05, and Wilson B-factors,
> 8.02 Å^2.
>
> Density maps looked great and the build refined easily enough (R/Rfree 
> 0.1939/0.2259)
> with a mean B-factor of 19.85, which according to phenix is lower than any
> other structure deposited in that resolution bin. Furthermore, the
> molprobity score is 0.83, and overall real-space correlation CC is 0.855.
>
> So my question is, can I feel comfortable depositing this?
>
> best regards
> Michael
>
> Chosen Solution:space group P 1 21 1
> Unit cell:44.93   41.90   45.83  90.00  115.57   90.00
> Number of batches in file:   1659
> The data do not appear to be twinned, from the L-test
> Overall InnerShell OuterShell
>
> Low resolution limit   41.34 41.34  2.49
>
> High resolution limit   2.40  8.98  2.40
>
>
> Rmerge  (within I+/I-) 0.231 0.084 0.782
>
> Rmerge  (all I+ and I-)0.266 0.099 0.983
>
> Rmeas (within I+/I-)   0.323 0.118 1.091
>
> Rmeas (all I+ & I-)0.317 0.118 1.167
>
> Rpim (within I+/I-)0.225 0.084 0.759
>
> Rpim (all I+ & I-) 0.171 0.063 0.623
>
> Rmerge in top intensity bin0.079- -
>
> Total number of observations   19901   362  2067
>
> Total number unique 6054   126   611
>
> Mean((I)/sd(I))  2.7   4.6   1.0
>
> Mn(I) half-set correlation CC(1/2) 0.958 0.991 0.570
>
> Completeness98.6  98.2  97.3
>
> Multiplicity 3.3   2.9   3.4
>
> Mean(Chi^2) 0.48  0.33  0.50
>
>
> Anomalous completeness  81.7  92.2  75.1
>
> Anomalous multiplicity   1.5   1.8   1.9
>
> DelAnom correlation between half-sets -0.003 0.041 0.045
>
> Mid-Slope of Anom Normal Probability   0.704   - -
>
>
> The anomalous signal appears to be weak so anomalous flag was left OFF
>
>
> Estimates of resolution limits: overall
>
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>
>from Mn(I/sd) >  1.50: limit =  2.67A
>
>from Mn(I/sd) >  2.00: limit =  2.87A
>
>
> Estimates of resolution limits in reciprocal lattice directions:
>
>   Along0.96 a* - 0.28 c*
>
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>
>from Mn(I/sd) >  1.50: limit =  2.40A  == maximum 
> resolution
>
>   Along k axis
>
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>
>from Mn(I/sd) >  1.50: limit =  2.86A
>
>   Along   -0.17 a* + 0.99 c*
>
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>
>from Mn(I/sd) >  1.50: limit =  2.98A
>
>
> Anisotropic deltaB (i.e. range of principal components), A^2:  8.62
>
>
> Average unit cell:44.93   41.90   45.83   90.00  115.57   90.00
>
> Space group: P 1 21 1
>
> Average mosaicity:   0.05
>
>
> Minimum and maximum SD correction factors: Fulls   1.27   1.28 Partials   
> 0.00   0.00
>
>
>
>
>
> Michael Jarva, PhD
> ACRF Chemical Biology Division
> The Walter and Eliza Hall Institute of Medical Research
>

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

2019-11-04 Thread Jrh Gmail

Dear Michael
The Rmerge in the strong intensity bin of 0.079 is untypically high it seems to 
me. 
Were the diffraction images underexposed? 
Best wishes
John

Emeritus Professor of Chemistry John R Helliwell DSc_Physics 



> On 3 Nov 2019, at 23:19, Michael Jarva  wrote:
> 
> 
> Hi CCP4BB,
> 
> I have some unusual crystal diffraction data I'd like to get your input on.
> 
> Almost a year ago I shot some small rods sticking out of a loop, so basically 
> no liquid around them - using the microfocus MX2 beamline at the australian 
> synchrotron, collected on an EIGER 16M detector.
> 
> The crystals diffracted weakly and was seemingly not viable at first glance 
> because of high Rmerge/Rpims. See the aimless summary at the bottom of this 
> post. This seemed to stem from a low spot intensity at low resolutions 
> (I/sd(I)=4.6), but since the CC1/2 was fine I went with it anyway.
> 
> Here I also noted an unusually low Mosaicity, 0.05, and Wilson B-factors, 
> 8.02 Å^2.
> 
> Density maps looked great and the build refined easily enough (R/Rfree 
> 0.1939/0.2259) with a mean B-factor of 19.85, which according to phenix is 
> lower than any other structure deposited in that resolution bin. Furthermore, 
> the molprobity score is 0.83, and overall real-space correlation CC is 0.855.
> 
> So my question is, can I feel comfortable depositing this? 
> 
> best regards
> Michael
> 
> Chosen Solution:space group P 1 21 1
> Unit cell:44.93   41.90   45.83  90.00  115.57   90.00
> Number of batches in file:   1659
> The data do not appear to be twinned, from the L-test
> Overall InnerShell OuterShell
> Low resolution limit   41.34 41.34  2.49
> High resolution limit   2.40  8.98  2.40
> 
> Rmerge  (within I+/I-) 0.231 0.084 0.782
> Rmerge  (all I+ and I-)0.266 0.099 0.983
> Rmeas (within I+/I-)   0.323 0.118 1.091
> Rmeas (all I+ & I-)0.317 0.118 1.167
> Rpim (within I+/I-)0.225 0.084 0.759
> Rpim (all I+ & I-) 0.171 0.063 0.623
> Rmerge in top intensity bin0.079- - 
> Total number of observations   19901   362  2067
> Total number unique 6054   126   611
> Mean((I)/sd(I))  2.7   4.6   1.0
> Mn(I) half-set correlation CC(1/2) 0.958 0.991 0.570
> Completeness98.6  98.2  97.3
> Multiplicity 3.3   2.9   3.4
> Mean(Chi^2) 0.48  0.33  0.50
> 
> Anomalous completeness  81.7  92.2  75.1
> Anomalous multiplicity   1.5   1.8   1.9
> DelAnom correlation between half-sets -0.003 0.041 0.045
> Mid-Slope of Anom Normal Probability   0.704   - -  
> 
> The anomalous signal appears to be weak so anomalous flag was left OFF
> 
> Estimates of resolution limits: overall
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>from Mn(I/sd) >  1.50: limit =  2.67A 
>from Mn(I/sd) >  2.00: limit =  2.87A 
> 
> Estimates of resolution limits in reciprocal lattice directions:
>   Along0.96 a* - 0.28 c*
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>from Mn(I/sd) >  1.50: limit =  2.40A  == maximum 
> resolution
>   Along k axis
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>from Mn(I/sd) >  1.50: limit =  2.86A 
>   Along   -0.17 a* + 0.99 c*
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>from Mn(I/sd) >  1.50: limit =  2.98A 
> 
> Anisotropic deltaB (i.e. range of principal components), A^2:  8.62
> 
> Average unit cell:44.93   41.90   45.83   90.00  115.57   90.00
> Space group: P 1 21 1
> Average mosaicity:   0.05
> 
> Minimum and maximum SD correction factors: Fulls   1.27   1.28 Partials   
> 0.00   0.00
> 
> 
> 
> 
> Michael Jarva, PhD
> ACRF Chemical Biology Division
> The Walter and Eliza Hall Institute of Medical Research
> 1G Royal Parade
> Parkville Victoria 3052
> Australia
> Phone: +61 3 9345 2493 
> Email: jarv...@wehi.edu.au | Web: http://www.wehi.edu.au/
> The ACRF Chemical Biology Division is supported by the
> Australian Cancer Research Foundation
> 
> ___ 
> 
> The information in this email is confidential and intended solely for the 
> addressee.
> You must not disclose, forward, print or use it without the permission of the 
> sender.
> 
> The Walter and Eliza Hall Institute ack

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

2019-11-05 Thread vincent Chaptal


Hi Michael,

I believe you are looking at the anisotropic B factor. 8 A2 is very low, 
you are all good.

The Wilson B is given by Truncate if I'm not mistaking.

Best regards
Vincent

Le 04/11/2019 à 00:18, Michael Jarva a écrit :

Hi CCP4BB,

I have some unusual crystal diffraction data I'd like to get your 
input on.


Almost a year ago I shot some small rods sticking out of a loop, so 
basically no liquid around them - using the microfocus MX2 beamline at 
the australian synchrotron, collected on an EIGER 16M detector.


The crystals diffracted weakly and was seemingly not viable at first 
glance because of high Rmerge/Rpims. See the aimless summary at the 
bottom of this post. This seemed to stem from a low spot intensity at 
low resolutions (I/sd(I)=4.6), but since the CC1/2 was fine I went 
with it anyway.


Here I also noted an unusually low Mosaicity, 0.05, and Wilson 
B-factors, 8.02 Å^2.


Density maps looked great and the build refined easily enough (R/Rfree 
0.1939/0.2259) with a mean B-factor of 19.85, which according to 
phenix is lower than any other structure deposited in that resolution 
bin. Furthermore, the molprobity score is 0.83, and overall real-space 
correlation CC is 0.855.


So my question is, can I feel comfortable depositing this?

best regards
Michael

Chosen Solution:    space group P 1 21 1
Unit cell:    44.93   41.90   45.83      90.00  115.57   90.00
Number of batches in file:   1659
The data do not appear to be twinned, from the L-test
Overall InnerShell OuterShell
Low resolution limit 41.34 41.34 2.49
High resolution limit 2.40 8.98 2.40
Rmerge (within I+/I-) 0.231 0.084 0.782
Rmerge (all I+ and I-) 0.266 0.099 0.983
Rmeas (within I+/I-) 0.323 0.118 1.091
Rmeas (all I+ & I-) 0.317 0.118 1.167
Rpim (within I+/I-) 0.225 0.084 0.759
Rpim (all I+ & I-) 0.171 0.063 0.623
Rmerge in top intensity bin 0.079 - -
Total number of observations 19901 362 2067
Total number unique 6054 126 611
Mean((I)/sd(I)) 2.7 4.6 1.0
Mn(I) half-set correlation CC(1/2) 0.958 0.991 0.570
Completeness 98.6 98.2 97.3
Multiplicity 3.3 2.9 3.4
Mean(Chi^2) 0.48 0.33 0.50
Anomalous completeness 81.7 92.2 75.1
Anomalous multiplicity 1.5 1.8 1.9
DelAnom correlation between half-sets -0.003 0.041 0.045
Mid-Slope of Anom Normal Probability 0.704 - -
The anomalous signal appears to be weak so anomalous flag was left OFF
Estimates of resolution limits: overall
from half-dataset correlation CC(1/2) > 0.30: limit = 2.40A == maximum 
resolution

from Mn(I/sd) > 1.50: limit = 2.67A
from Mn(I/sd) > 2.00: limit = 2.87A
Estimates of resolution limits in reciprocal lattice directions:
Along 0.96 a* - 0.28 c*
from half-dataset correlation CC(1/2) > 0.30: limit = 2.40A == maximum 
resolution

from Mn(I/sd) > 1.50: limit = 2.40A == maximum resolution
Along k axis
from half-dataset correlation CC(1/2) > 0.30: limit = 2.40A == maximum 
resolution

from Mn(I/sd) > 1.50: limit = 2.86A
Along -0.17 a* + 0.99 c*
from half-dataset correlation CC(1/2) > 0.30: limit = 2.40A == maximum 
resolution

from Mn(I/sd) > 1.50: limit = 2.98A
Anisotropic deltaB (i.e. range of principal components), A^2: 8.62
Average unit cell: 44.93 41.90 45.83 90.00 115.57 90.00
Space group: P 1 21 1
Average mosaicity: 0.05
Minimum and maximum SD correction factors: Fulls 1.27 1.28 Partials 
0.00 0.00





Michael Jarva, PhD
ACRF Chemical Biology Division

The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade
Parkville Victoria 3052
Australia

Phone: +61 3 9345 2493 
Email: jarv...@wehi.edu.au | Web: http://www.wehi.edu.au/

The ACRF Chemical Biology Division is supported by the

Australian Cancer Research Foundation


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[ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

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