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Sandbox7 Eric Martz

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Proposed title: <span style="font-size:150%">Temperature vs. Resolution</span>
Proposed title: <span style="font-size:150%">Temperature vs. Resolution</span>
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==Summary==
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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).
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{| class="wikitable"
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|+ SUMMARY<br>[[Temperature value]] vs. [[Resolution]]
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|-
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! rowspan="2"|Resolution
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! colspan="3"|Temperature values
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|-
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! Min !! Average !! Max
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|-
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| Min || 2-7 || 5.6
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|-
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| Av || 14-31 || 20.3
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|-
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| Max || 59-104 || 73.9
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|}
==1.4 &Aring;ngstroms Resolution==
==1.4 &Aring;ngstroms Resolution==
<div style="float:left">
<div style="float:left">

Revision as of 21:47, 27 June 2011

Please do not edit this page. Thank you, User:Eric Martz, June 2011.

Proposed title: Temperature vs. Resolution

Contents

Summary

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).

SUMMARY
Temperature value vs. Resolution
Resolution Temperature values
Min Average Max
Min 2-7 5.6
Av 14-31 20.3
Max 59-104 73.9

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".

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