Thank you everyone for your contributions that help me understand more.
Let me try to rephrase my initial post:
Say that I have diffraction up to 6A resolution, I would say that my
crystal is decently ordered (see the glass half full), enough for
observing repeating units that do not fluctuate too much. Given the
biology of my system, I would aim for secondary structures but it could
be something else. Importantly, I have a crystal and therefore some
order, but unfortunately my order is not high enough to allow for
diffraction at higher resolution.
Now, say that I manage to optimize my crystal to gain diffraction in one
direction to 3.5A, while the other one still stalls at 6A (I am not
talking about anisotropy). I would thus say that my optimization helped
me to gain order in one direction, or reduce the flexibility in this
particular direction of reciprocal/real space.
I am tempted to push the analysis further in terms of protein
deformability. Does this sound reasonable?
I've been asked for the link to James Holton's web page:
http://bl831.als.lbl.gov/~jamesh/movies/
http://proteopedia.org/wiki/index.php/Resolution
All the best
Vincent
On 29/11/2017 05:05, Daniel M. Himmel, Ph. D. wrote:
Dear Vincent,
The resolution limit of reflections is a consequence of the closest
distances in the structure that are consistent repeating units in the
crystal lattice. This is not automatically linked to any particular
features of a structure per se. In addition, while some of the structural
fine features may be ordered at a particular resolution, other of those
same features (e.g., different helices in a protein) may be disordered,
depending on the properties of the particular protein and its crystal
packing in a particular crystal form. What you can say is what level
of structural detail is generally visible at a particular resolution, as
a "rule of thumb", but even here, something can be visible and still
open to interpretation when building the structure into the electron
density.
In my experience, at about 5 A, you can start to make out individual
alpha helices (appearing as cylinders) and beta sheets.
At around 4 A, you can approximately assign some of the more
bulky side chains if they are ordered (which they might not be).
At 3 A, you can see a lot more side chain detail (and I've published
structures at this resolution), but you have to be very careful in
assignments to avoid errors. At 2 A, details tend to be a lot clearer.
If your resolution is under 1 A, you begin to see details about the
electron clouds around an atom that sometimes can be useful in
supporting mechanistic conclusions. All this does not allow you
to make a general statement about what type of structural element
is always ordered.
I hope this helps.
-Daniel
________
Daniel M. Himmel, Ph. D.
On Tue, Nov 28, 2017 at 9:44 AM, vincent Chaptal
<vincent.chap...@ibcp.fr <mailto:vincent.chap...@ibcp.fr>> wrote:
Hi,
I've been searching but can't find what I am looking for so I
thought I ask specialists.
I am curious about the link between resolution limits of
reflections on the detector, and what features are ordered in real
space.
I saw the great movie by James Holton on resolution and features
in the electron density map, but I am looking for something more
general.
I am thinking that a reflection on the detector originates from
something ordered within the crystal. The level of order would be
different at different resolution.
If you can help me fill the void in this phrase:
I see spots at __A resolution, therefore I know that _____
features are ordered in my crystal.
intuitively, I would build the following scale:
20A : the envelope is ordered
10A: a finer envelope is ordered
6A: alpha helices are ordered
4-5A: beta sheets are ordered and some residues
3-4A: residues start to be ordered
>3A: more and more order.
Has this been described somewhere? I would appreciate any comments
and reevaluation of this scale.
Thank you in advance.
All the best
Vincent
--
Vincent Chaptal, PhD
Institut de Biologie et Chimie des Protéines
Drug Resistance and Membrane Proteins Laboratory
7 passage du Vercors
<https://maps.google.com/?q=7+passage+du+Vercors%C2%A0%0D+69007+LYON%0D+FRANCE&entry=gmail&source=g><https://maps.google.com/?q=7+passage+du+Vercors%C2%A0%0D+69007+LYON%0D+FRANCE&entry=gmail&source=g>
69007 LYON
<https://maps.google.com/?q=7+passage+du+Vercors%C2%A0%0D+69007+LYON%0D+FRANCE&entry=gmail&source=g>
FRANCE
<https://maps.google.com/?q=7+passage+du+Vercors%C2%A0%0D+69007+LYON%0D+FRANCE&entry=gmail&source=g>
+33 4 37 65 29 01 <tel:+33%204%2037%2065%2029%2001>
http://www.ibcp.fr
--
Vincent Chaptal, PhD
Institut de Biologie et Chimie des Protéines
Drug Resistance and Membrane Proteins Laboratory
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 01
http://www.ibcp.fr
