Temperature value vs. resolution

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(→Summary)
Line 1: Line 1:
-
In brief, the ''temperature value'' (also called ''B factor'') for an atom in a [[X-ray crystallography|crystallographic]] model is a measure of the uncertainty of the position of that atom. (For more, see [[Temperature value]].) The [[resolution]] is an average measure of the uncertainty for all atoms in the model. Results from a very small sample, below, suggest that the average temperature value is positively correlated with the resolution.
+
In brief, the ''temperature value'' (also called ''B factor'') for an atom in a [[X-ray crystallography|crystallographic]] model is a measure of the uncertainty of the position of that atom. (For more, see [[Temperature value]].) The [[resolution]] is an average measure of the uncertainty for all atoms in the model. Results from a very small sample, below, suggest that the average temperature values of models are positively correlated with their resolutions.
==Summary==
==Summary==

Revision as of 22:03, 27 June 2011

In brief, the temperature value (also called B factor) for an atom in a crystallographic model is a measure of the uncertainty of the position of that atom. (For more, see Temperature value.) The resolution is an average measure of the uncertainty for all atoms in the model. Results from a very small sample, below, suggest that the average temperature values of models are positively correlated with their resolutions.

Contents

Summary

Caution: The following results are based on very small samples of 7-8 PDB files, excluding a few cases that appeared to be outliers (see details below). The median resolution in the Protein Data Bank is 2.19 Å (on June 27, 2011).

SUMMARY
Temperature value vs. Resolution
Resolution Averages of Temperature Values
N = 7-8
Min Average[1] Max
1.4 Å 6 20 74
2.0 Å 12 30 66
3.5 Å 18 62 169
  1. ↑ Average, over 7-8 models, of the average values per model.

1.4 Ångstroms Resolution

Resolution 1.4 Ångstroms
Min/Av/Max: Temperature values. Examples selected for low or high R/Rfree.

PDB ID Deposition R R free Min Av Max Notes
2c5a 2005 0.105 0.140 2 14 68
2xon 2010 0.119 0.167 5 17 59
1hmt 1994 0.14 --- 7 20 104
1ubm 2003 0.117 0.189 10 24 158 Outlier
3e8o 2008 0.130 0.163 7 18 60
3mgn 2010 0.262 0.288 6 31 93
403d 1998 0.242 0.316 6 25 69 DNA
2a4x 2005 0.222 0.264 6 17 64 Excluding ligand[1]
SUMMARY
Temperature values
for resolution 1.4 Å
Column Range[2] Average[2]
N=7
Min 2-7 5.6
Av 14-31 20.3
Max 59-104 73.9
  1. ↑ A ligand (29 atoms; 1.2% of all 2,352 atoms) had an average temperature of 80.
  2. ↑ 2.0 2.1 Excludes rows designated as outliers.

2.0 Ångstroms Resolution

2.19 Ångstroms is the median resolution in the Protein Data Bank as of June 27, 2011.

Resolution 2.0 Ångstroms
Min/Av/Max: Temperature values. Examples selected for low or high R/Rfree.

PDB ID Deposition R R free Min Av Max Notes
3nt6 2010 0.124 0.155 2 36 78
1tbt 2004 0.130 0.184 7 21 59
1qno 1999 0.126 0.200 2 12 72
1vra 2005 0.141 0.158 11 30 64 SG[1]
1yze 2005 0.325 0.367 22 22 22 Outlier
1m3y 2002 0.342 0.352 16 34 67
3d0m 2008 0.295 0.361 30 62 130 RNA, Outlier
2w2v 2008 0.283 0.345 17 29 59
3dvv 2008 0.268 0.277 26 45 66 RNA
SUMMARY
Temperature values
for resolution 2.0 Å
Column Range[2] Average[2]
N=7
Min 2-26 11.6
Av 12-45 29.6
Max 59-78 66.4
  1. ↑ Structural genomics entry.
  2. ↑ 2.0 2.1 Excludes rows designated as outliers.

3.5 Ångstroms Resolution

Resolution 3.5 Ångstroms
Min/Av/Max: Temperature values. Examples selected for low or high R/Rfree.
The median free R for resolution 3.5 Å is 0.29 (June, 2011).

PDB ID Deposition R R free Min Av Max Notes[1]
3m2k 2010 0.180 0.236 2 14 78
2qls 2007 0.203 0.293 2 23 84
1xcq 2004 0.195 0.264 24 57 222
1xgo 1997 0.182 0.274 2 31 108
2pzx 2007 0.376 0.407 0 58 198
2j7o 2006 0.353 0.360 37 119 150
2vrt 2008 0.321 0.351 64 117 317
2x6k 2010 0.238 0.296 15 75 195
SUMMARY
Temperature values
for resolution 3.5 Å
Column Range[2] Average[2]
N=8
Min 0-64 18.3
Av 14-119 61.8
Max 78-317 169
  1. ↑ No entries containing only nucleic acids have resolution 3.5 and R value <0.4.
  2. ↑ 2.0 2.1 Excludes rows designated as outliers.

Methods

At Temperature color schemes is a Jmol script that reports the min/av/max temperature values in a PDB file. These values can also be reported with the following commands:

  • print {*}.temperature.min
  • print {*}.temperature
  • print {*}.temperature.max

where {*} means "all atoms".

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

Retrieved from "http://52.214.119.220/wiki/index.php/Temperature_value_vs._resolution"
Personal tools