[ccp4bb] Bond Length Outliers (correction)
Ahh yes, I looked at the wrong line. My Rmsd bond angle is 2.55 degrees (not bond length). MolProbity states that my only abnormal angle is 124.23 degrees between O--C--N of an Arg. Real Space Refinement does not change anything and Regularizing the zone completely distorts the backbone. Any suggestions on how to fix this? --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 - Original Message - From: Bernard D. Santarsiero b...@uic.edu To: Greg Costakes gcost...@purdue.edu Sent: Thursday, February 16, 2012 11:42:55 AM Subject: Re: [ccp4bb] Bond Length Outliers Greg, Your RMSD on bond lengths should be around 0.01A (your structure vs. idealized library), and the RMSD on bond angles should be around 1.5deg. You must be using an incorrect value of the weight factor between structure factors and geometric factors, and relying too heavily on structure factors. Bernie On Thu, February 16, 2012 10:31 am, Greg Costakes wrote: I am currently in the final steps of refining a 1.3A structure and am coming across a slight problem. According the the pdb file, I have an Rmsd bond length of 2.55. MolProbity identifies three outliers which correspond to the bond lengths of: Asp: C--O , bond length = 1.2A Arg: C--O , bond length = 1.15A Ala: N--Ca , bond length = 1.43A Real space refinement in Coot does not help and if I Regularize the zone it completely distorts the backbone. So my question is, how do I fix these bond length outliers? Do I need to be concerned with them? Any advice will be much appreciated. Thank you! --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907
Re: [ccp4bb] Bond Length Outliers (correction)
Hi, If I remember correctly this angle is for the planarity of the peptide bond. Maybe you have a real deviation which might occur not so seldom than expected. You have a quite high resolution. If the density is really convincing then you may accept this outlier. Not every outlier is a mistake. However with 2.55° the r.m.s.d. for your angles is quite high I think. Christian Am Donnerstag 16 Februar 2012 18:00:10 schrieb Greg Costakes: Ahh yes, I looked at the wrong line. My Rmsd bond angle is 2.55 degrees (not bond length). MolProbity states that my only abnormal angle is 124.23 degrees between O--C--N of an Arg. Real Space Refinement does not change anything and Regularizing the zone completely distorts the backbone. Any suggestions on how to fix this? --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 --- - - Original Message - From: Bernard D. Santarsiero b...@uic.edu To: Greg Costakes gcost...@purdue.edu Sent: Thursday, February 16, 2012 11:42:55 AM Subject: Re: [ccp4bb] Bond Length Outliers Greg, Your RMSD on bond lengths should be around 0.01A (your structure vs. idealized library), and the RMSD on bond angles should be around 1.5deg. You must be using an incorrect value of the weight factor between structure factors and geometric factors, and relying too heavily on structure factors. Bernie On Thu, February 16, 2012 10:31 am, Greg Costakes wrote: I am currently in the final steps of refining a 1.3A structure and am coming across a slight problem. According the the pdb file, I have an Rmsd bond length of 2.55. MolProbity identifies three outliers which correspond to the bond lengths of: Asp: C--O , bond length = 1.2A Arg: C--O , bond length = 1.15A Ala: N--Ca , bond length = 1.43A Real space refinement in Coot does not help and if I Regularize the zone it completely distorts the backbone. So my question is, how do I fix these bond length outliers? Do I need to be concerned with them? Any advice will be much appreciated. Thank you! - -- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 - ---
Re: [ccp4bb] Bond Length Outliers (correction)
Using the Protein Geometry Database (pgd.science.oregonstate.edu) I looked up all Arg residues in models with resolution of 1.3 A or better and found 5920 examples. The mean value of the O-C-N angle (and I'm assuming that the O and C atoms are in the Arg) is 122.6 deg with a sigma of 1.1 deg. 338 of them have a value greater than 124.23 deg, or about 6%. It doesn't look to me that this piece of structure is an outlier. Regularizing may move atoms out of density but it shouldn't distort anything, it should make it, cough, more regular. If regularizing is doing something bad there is a problem with the regularizer not the structure. Does you model have any ligands that might have horrible angles but not be reported by MolProbity? Dale Tronrud On 02/16/12 09:00, Greg Costakes wrote: Ahh yes, I looked at the wrong line. My Rmsd bond angle is 2.55 degrees (not bond length). MolProbity states that my only abnormal angle is 124.23 degrees between O--C--N of an Arg. Real Space Refinement does not change anything and Regularizing the zone completely distorts the backbone. Any suggestions on how to fix this? --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 *From: *Bernard D. Santarsiero b...@uic.edu *To: *Greg Costakes gcost...@purdue.edu *Sent: *Thursday, February 16, 2012 11:42:55 AM *Subject: *Re: [ccp4bb] Bond Length Outliers Greg, Your RMSD on bond lengths should be around 0.01A (your structure vs. idealized library), and the RMSD on bond angles should be around 1.5deg. You must be using an incorrect value of the weight factor between structure factors and geometric factors, and relying too heavily on structure factors. Bernie On Thu, February 16, 2012 10:31 am, Greg Costakes wrote: I am currently in the final steps of refining a 1.3A structure and am coming across a slight problem. According the the pdb file, I have an Rmsd bond length of 2.55. MolProbity identifies three outliers which correspond to the bond lengths of: Asp: C--O , bond length = 1.2A Arg: C--O , bond length = 1.15A Ala: N--Ca , bond length = 1.43A Real space refinement in Coot does not help and if I Regularize the zone it completely distorts the backbone. So my question is, how do I fix these bond length outliers? Do I need to be concerned with them? Any advice will be much appreciated. Thank you! --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907
Re: [ccp4bb] Bond Length Outliers (correction)
Btw, re other sources of deviation: Molprobity does not report geometry deviations beyond CB. The RUN500 command from CCP4i does. BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale Tronrud Sent: Thursday, February 16, 2012 10:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Bond Length Outliers (correction) Using the Protein Geometry Database (pgd.science.oregonstate.edu) I looked up all Arg residues in models with resolution of 1.3 A or better and found 5920 examples. The mean value of the O-C-N angle (and I'm assuming that the O and C atoms are in the Arg) is 122.6 deg with a sigma of 1.1 deg. 338 of them have a value greater than 124.23 deg, or about 6%. It doesn't look to me that this piece of structure is an outlier. Regularizing may move atoms out of density but it shouldn't distort anything, it should make it, cough, more regular. If regularizing is doing something bad there is a problem with the regularizer not the structure. Does you model have any ligands that might have horrible angles but not be reported by MolProbity? Dale Tronrud On 02/16/12 09:00, Greg Costakes wrote: Ahh yes, I looked at the wrong line. My Rmsd bond angle is 2.55 degrees (not bond length). MolProbity states that my only abnormal angle is 124.23 degrees between O--C--N of an Arg. Real Space Refinement does not change anything and Regularizing the zone completely distorts the backbone. Any suggestions on how to fix this? -- - Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 -- -- -- -- *From: *Bernard D. Santarsiero b...@uic.edu *To: *Greg Costakes gcost...@purdue.edu *Sent: *Thursday, February 16, 2012 11:42:55 AM *Subject: *Re: [ccp4bb] Bond Length Outliers Greg, Your RMSD on bond lengths should be around 0.01A (your structure vs. idealized library), and the RMSD on bond angles should be around 1.5deg. You must be using an incorrect value of the weight factor between structure factors and geometric factors, and relying too heavily on structure factors. Bernie On Thu, February 16, 2012 10:31 am, Greg Costakes wrote: I am currently in the final steps of refining a 1.3A structure and am coming across a slight problem. According the the pdb file, I have an Rmsd bond length of 2.55. MolProbity identifies three outliers which correspond to the bond lengths of: Asp: C--O , bond length = 1.2A Arg: C--O , bond length = 1.15A Ala: N--Ca , bond length = 1.43A Real space refinement in Coot does not help and if I Regularize the zone it completely distorts the backbone. So my question is, how do I fix these bond length outliers? Do I need to be concerned with them? Any advice will be much appreciated. Thank you! -- - Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 -- --
