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Sandbox7 Eric Martz

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<font color="red">Please do not edit this page. Thank you, [[User:Eric Martz]], June 2011.</font>
<font color="red">Please do not edit this page. Thank you, [[User:Eric Martz]], June 2011.</font>
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Proposed title: <span style="font-size:150%">Temperature vs. Resolution</span>
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(available)
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==Summary==
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'''Caution:''' The following results are based on <font color="red">very small samples</font> 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 &Aring; (on June 27, 2011).
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{| class="wikitable" style="text-align:center"
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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"|Averages of Temperature Values<br>N = 7-8
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! Min !! Average !! Max
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|-
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| 1.4 &Aring; || 6 || 20 || 74
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|-
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| 2.0 &Aring; || 12 || 30 || 66
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|-
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| 3.5 &Aring; || 18 || 62 || 169
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|}
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==1.4 &Aring;ngstroms Resolution==
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<div style="float:left">
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<center>
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<span style="font-size:125%;">[[Resolution]] 1.4 &Aring;ngstroms</span><br>
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Min/Av/Max: [[Temperature values]]. Examples selected for low or high R/Rfree.
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</center>
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{| class="wikitable sortable"
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|-
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! [[PDB ID]] !! Deposition !! [[R value|R]] !! [[Free R|R free]] !! Min !! Av !! Max !! Notes
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| [[2c5a]] || 2005 || 0.105 || 0.140 || 2 || 14 || 68 ||
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| [[2xon]] || 2010 || 0.119 || 0.167 || 5 || 17 || 59 ||
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|-
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| [[1hmt]] || 1994 || 0.14 || --- || 7 || 20 || 104 ||
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|- style="color:gray;"
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| [[1ubm]] || 2003 || 0.117 || 0.189 || 10 || 24 || 158 || Outlier
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| [[3e8o]] || 2008 || 0.130 || 0.163 || 7 || 18 || 60 ||
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| [[3mgn]] || 2010 || 0.262 || 0.288 || 6 || 31 || 93 ||
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|-
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| [[403d]] || 1998 || 0.242 || 0.316 || 6 || 25 || 69 || DNA
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|-
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| [[2a4x]] || 2005 || 0.222 || 0.264 || 6 || 17 || 64 || Excluding ligand<ref>A ligand (29 atoms; 1.2% of all 2,352 atoms) had an average temperature of 80.</ref>
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|}
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</div>
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<div style="float:right;margin-top:0px;" >
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{| class="wikitable"
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|+ SUMMARY<br>Temperature values<br>for [[resolution]] 1.4 &Aring;
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|-
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! Column !! Range<ref name="xo">Excludes rows designated as outliers.</ref> !! Average<ref name="xo" /><br>N=7
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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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| Max || 59-104 || 73.9
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|}
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</div>
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{{Clear}}
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<references />
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==2.0 &Aring;ngstroms Resolution==
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2.19 &Aring;ngstroms is the median [[resolution]] in the [[Protein Data Bank]] as of June 27, 2011.
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<div style="float:left">
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<center>
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<span style="font-size:125%;">[[Resolution]] 2.0 &Aring;ngstroms</span><br>
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Min/Av/Max: [[Temperature values]]. Examples selected for low or high R/Rfree.
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</center>
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{| class="wikitable sortable"
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|-
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! [[PDB ID]] !! Deposition !! [[R value|R]] !! [[Free R|R free]] !! Min !! Av !! Max !! Notes
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| [[3nt6]] || 2010 || 0.124 || 0.155 || 2 || 36 || 78 ||
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|-
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| [[1tbt]] || 2004 || 0.130 || 0.184 || 7 || 21 || 59 ||
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|-
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| [[1qno]] || 1999 || 0.126 || 0.200 || 2 || 12 || 72 ||
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|-
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| [[1vra]] || 2005 ||0.141 || 0.158 || 11 || 30 || 64 || SG<ref>Structural genomics entry.</ref>
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|-style="color:gray;"
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|[[1yze]] || 2005 || 0.325 || 0.367 || 22 || 22 || 22 || Outlier
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|-
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| [[1m3y]] || 2002 || 0.342 || 0.352 || 16 || 34 || 67 ||
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|-style="color:gray;"
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| [[3d0m]] || 2008 || 0.295 || 0.361 || 30 || 62 || 130 || RNA, Outlier
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|-
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| [[2w2v]] || 2008 || 0.283 || 0.345 || 17 || 29 || 59 ||
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|-
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| [[3dvv]] || 2008 || 0.268 || 0.277 || 26 || 45 || 66 || RNA
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|}
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</div>
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<div style="float:right;margin-top:0px;" >
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{| class="wikitable"
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|+ SUMMARY<br>Temperature values<br>for [[resolution]] 2.0 &Aring;
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|-
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! Column !! Range<ref name="xo">Excludes rows designated as outliers.</ref> !! Average<ref name="xo" /><br>N=7
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|-
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| Min || 2-26 || 11.6
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| Av || 12-45 || 29.6
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| Max || 59-78 || 66.4
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|}
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</div>
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{{Clear}}
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<references />
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==3.5 &Aring;ngstroms Resolution==
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<div style="float:left">
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<center>
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<span style="font-size:125%;">[[Resolution]] 3.5 &Aring;ngstroms</span>
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<br>
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Min/Av/Max: [[Temperature values]]. Examples selected for low or high R/Rfree.
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<br>
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The median [[free R]] for resolution 3.5 &Aring; is 0.29 (June, 2011).
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</center>
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{| class="wikitable sortable"
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|-
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! [[PDB ID]] !! Deposition !! [[R value|R]] !! [[Free R|R free]] !! Min !! Av !! Max !! Notes<ref>No entries containing only nucleic acids have resolution 3.5 and R value <0.4.</ref>
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| [[3m2k]] || 2010 || 0.180 || 0.236 || 2 || 14 || 78 ||
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|-
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| [[2qls]] || 2007 || 0.203 || 0.293 || 2 || 23 || 84 ||
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|-
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| [[1xcq]] || 2004 || 0.195 || 0.264 || 24 || 57 || 222 ||
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|-
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| [[1xgo]] || 1997 || 0.182 || 0.274 || 2 || 31 || 108 ||
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|-
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| [[2pzx]] || 2007 || 0.376 || 0.407 || 0 || 58 || 198 ||
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|-
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| [[2j7o]] || 2006 || 0.353 || 0.360 || 37 || 119 || 150 ||
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| [[2vrt]] || 2008 || 0.321 || 0.351 || 64 || 117 || 317||
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|-
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| [[2x6k]] || 2010 || 0.238 || 0.296 || 15 || 75 || 195||
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|}
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</div>
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<div style="float:right;margin-top:0px;" >
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{| class="wikitable"
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|+ SUMMARY<br>Temperature values<br>for [[resolution]] 3.5 &Aring;
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|-
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! Column !! Range<ref name="xo">Excludes rows designated as outliers.</ref> !! Average<ref name="xo" /><br>N=8
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|-
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| Min || 0-64 || 18.3
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| Av || 14-119 || 61.8
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|-
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| Max || 78-317 || 169
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|}
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</div>
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{{Clear}}
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<references />
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==Methods==
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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:
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*print {*}.temperature.min
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*print {*}.temperature
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*print {*}.temperature.max
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where {*} means "all atoms".
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Revision as of 22:12, 27 June 2011

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

(available)

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox7_Eric_Martz"
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