Difference between revisions of "Gaucher Disease: Task 09 - Lab Journal"
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|[http://www.pdb.org/pdb/files/3GXI.pdb 3GXI] || 1.84 || A/B/C/D || 40-536 (92.7%) || 1-39? || 0.193 || 0.231 || 5.5 || ? |
|[http://www.pdb.org/pdb/files/3GXI.pdb 3GXI] || 1.84 || A/B/C/D || 40-536 (92.7%) || 1-39? || 0.193 || 0.231 || 5.5 || ? |
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− | |[http://www.pdb.org/pdb/files/2V3F.pdb 2V3F] || 1.95 || A/B || 40-536 (92.7%) || 1-39? || 0.154 || 0.196 || 6.5 || 100 |
+ | |[http://www.pdb.org/pdb/files/2V3F.pdb 2V3F] || 1.95 || A/B || 40-536 (92.7%) || 1-39? || 0.154 || 0.196 || '''6.5''' || 100 |
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− | |[http://www.pdb.org/pdb/files/2V3D.pdb 2V3D] || 1.96 || A/B || 40-536 (92.7%) || 1-39? || 0.157 || 0.208 || 6.5 || 100 |
+ | |[http://www.pdb.org/pdb/files/2V3D.pdb 2V3D] || 1.96 || A/B || 40-536 (92.7%) || 1-39? || 0.157 || 0.208 || '''6.5''' || 100 |
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|[http://www.pdb.org/pdb/files/1OGS.pdb 1OGS] || 2.0 || A-/B || 40-536 (92.7%) || 1-39? || 0.195 || 0.230 || 4.6 || 100 |
|[http://www.pdb.org/pdb/files/1OGS.pdb 1OGS] || 2.0 || A-/B || 40-536 (92.7%) || 1-39? || 0.195 || 0.230 || 4.6 || 100 |
Revision as of 13:54, 28 August 2013
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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 | Covered residues | Missing residues | R-Value(obs.) | R-Free | pH | Temperature (K) |
---|---|---|---|---|---|---|---|---|
2NT0 | 1.79 | A/B/C/D | 40-536 (92.7%) | 1-39? | 0.181 | 0.215 | 4.5 | 100 |
3GXI | 1.84 | A/B/C/D | 40-536 (92.7%) | 1-39? | 0.193 | 0.231 | 5.5 | ? |
2V3F | 1.95 | A/B | 40-536 (92.7%) | 1-39? | 0.154 | 0.196 | 6.5 | 100 |
2V3D | 1.96 | A/B | 40-536 (92.7%) | 1-39? | 0.157 | 0.208 | 6.5 | 100 |
1OGS | 2.0 | A-/B | 40-536 (92.7%) | 1-39? | 0.195 | 0.230 | 4.6 | 100 |
</figtable>