Difference between revisions of "Gaucher Disease: Task 09 - Lab Journal"
Kalemanovm (talk | contribs) (→1. Choose a structure to work with) |
Kalemanovm (talk | contribs) (→1. Choose a structure to work with) |
||
Line 36: | Line 36: | ||
===1. Choose a structure to work with=== |
===1. Choose a structure to work with=== |
||
− | In the former tasks, we worked with the reference structure 1OGS, because it has no gaps - but an offset of 39 residues at the N terminus, as all structures for our protein P04062 referenced in [http://www.uniprot.org/uniprot/P04062 | UniProt] - and has a pretty low resolution of 2.0 Å. However, there are four other structures with a lower resolution (all resolved using the X-ray method). We compare 1OGS and those four structures for the resolution, coverage and gaps, R-factor, R-free and pH-value at which the structure was resolved in the following table. |
+ | In the former tasks, we worked with the reference structure 1OGS, because it has no gaps - but an offset of 39 residues at the N terminus, as all structures for our protein P04062 referenced in [http://www.uniprot.org/uniprot/P04062 | UniProt] - and has a pretty low resolution of 2.0 Å. However, there are four other structures with a lower resolution (all resolved using the X-ray diffraction method). We compare 1OGS and those four structures for the resolution, coverage and gaps, R-factor, R-free and pH-value at which the structure was resolved in the following table. |
<figtable id="structure_choice"> |
<figtable id="structure_choice"> |
||
{|class="colBasic2" |
{|class="colBasic2" |
||
− | !PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH || Temperature (Kelvin) |
+ | !PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor(obs.) || R-free || pH || Temperature (Kelvin) |
|- |
|- |
||
− | |1OGS || 2.0 || A-/B || 40-536 || no || 0.195 |
+ | |[http://www.pdb.org/pdb/files/1OGS.pdb | 1OGS] || 2.0 || A-/B || 40-536 || no || 0.195 || 0.230 || 4.6 || 100 |
|- |
|- |
||
− | | |
+ | |[http://www.pdb.org/pdb/files/2NT0.pdb | 2NT0] || 1.79 || A/B/C/D || 40-536 || Gaps || 0.181 || 0.215 || 4.5 || 100 |
|- |
|- |
||
− | |PDB-ID || Resolution (Å) || Chain || |
+ | |PDB-ID || Resolution (Å) || Chain || 40-536 || Gaps || R-factor || R-free || pH || |
|- |
|- |
||
− | |PDB-ID || Resolution (Å) || Chain || |
+ | |PDB-ID || Resolution (Å) || Chain || 40-536 || Gaps || R-factor || R-free || pH || |
|- |
|- |
||
− | |PDB-ID || Resolution (Å) || Chain || |
+ | |PDB-ID || Resolution (Å) || Chain || 40-536 || Gaps || R-factor || R-free || pH || |
|} |
|} |
||
<center><small>'''<caption>''' Comparison of the resolution top five PDB structures according to different other criteria.</caption></small></center> |
<center><small>'''<caption>''' Comparison of the resolution top five PDB structures according to different other criteria.</caption></small></center> |
Revision as of 13:20, 28 August 2013
<css>
table.colBasic2 { margin-left: auto; margin-right: auto; border: 1px solid black; border-collapse:collapse; }
.colBasic2 th,td { padding: 3px; border: 1px solid black; }
.colBasic2 td { text-align:left; }
/* for orange try #ff7f00 and #ffaa56 for blue try #005fbf and #aad4ff
maria's style blue: #adceff grey: #efefef
- /
.colBasic2 tr th { background-color:#efefef; color: black;} .colBasic2 tr:first-child th { background-color:#adceff; color:black;}
</css>
This page is under construction.
Contents
Preparation
1. Choose a structure to work with
In the former tasks, we worked with the reference structure 1OGS, because it has no gaps - but an offset of 39 residues at the N terminus, as all structures for our protein P04062 referenced in | UniProt - and has a pretty low resolution of 2.0 Å. However, there are four other structures with a lower resolution (all resolved using the X-ray diffraction method). We compare 1OGS and those four structures for the resolution, coverage and gaps, R-factor, R-free and pH-value at which the structure was resolved in the following table.
<figtable id="structure_choice">
PDB-ID | Resolution (Å) | Chain | Positions | Gaps | R-factor(obs.) | R-free | pH | Temperature (Kelvin) |
---|---|---|---|---|---|---|---|---|
1OGS] | 2.0 | A-/B | 40-536 | no | 0.195 | 0.230 | 4.6 | 100 |
2NT0] | 1.79 | A/B/C/D | 40-536 | Gaps | 0.181 | 0.215 | 4.5 | 100 |
PDB-ID | Resolution (Å) | Chain | 40-536 | Gaps | R-factor | R-free | pH | |
PDB-ID | Resolution (Å) | Chain | 40-536 | Gaps | R-factor | R-free | pH | |
PDB-ID | Resolution (Å) | Chain | 40-536 | Gaps | R-factor | R-free | pH |
</figtable>