Difference between revisions of "Fabry:Structure-based mutation analysis"
Rackersederj (talk | contribs) (→Preparation) |
Rackersederj (talk | contribs) (→Preparation) |
||
| Line 1: | Line 1: | ||
== Preparation == |
== Preparation == |
||
| − | <div style="float:left; border:thin solid lightgrey; margin: 0px |
+ | <div style="float:left; border:thin solid lightgrey; margin: 0px 20px 0px 0px;"> |
| − | <figtable id="tab: |
+ | <figtable id="tab:Prep"> |
| + | <caption>All available PDB structures assigned to the Uniprot entry [http://www.uniprot.org/uniprot/P06280 P06280] along with the according Resolution,<br> Coverage and R-factor. The R-factor was obtained from the PDBsum page.</caption> |
||
| − | <caption>ADD CAPTION HERE</caption> |
||
{| class="wikitable sortable" style="border-collapse: collapse; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0" |
{| class="wikitable sortable" style="border-collapse: collapse; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0" |
||
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Entry |
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Entry |
||
| Line 161: | Line 161: | ||
</figtable> |
</figtable> |
||
</div> |
</div> |
||
| + | We chose to use the structure 3HG3, since it has the best resolution (1.90 Å) and the second best R-factor (see <xr id="tab:Prep"/>). The best R-factor, which is a measure of the agreement between the crystallographic model and the experimental X-ray diffraction data <ref>R-factor (crystallography) (May 17, 2012) [http://en.wikipedia.org/wiki/R-factor_%28crystallography%29 http://en.wikipedia.org/wiki/R-factor_%28crystallography%29], June 20, 2012</ref>, could be achieved with the structure 3HG4, but it has a resolution of 2.30 Å and hence we decided to use 3HG3. All structures cover the protein completely except for the signal peptide from position 1 to 31. |
||
<br style="clear:both"> |
<br style="clear:both"> |
||
Revision as of 09:01, 20 June 2012
Contents
Preparation
<figtable id="tab:Prep">
All available PDB structures assigned to the Uniprot entry P06280 along with the according Resolution,
Coverage and R-factor. The R-factor was obtained from the PDBsum page.
| Entry | Method | Resolution (Å) | Chain | Positions | PDBsum | PDB | R-factor |
|---|---|---|---|---|---|---|---|
| 1R46 | X-ray | 3.25 | A/B | 32-429 | [»] | [»] | 0.262 |
| 1R47 | X-ray | 3.45 | A/B | 32-429 | [»] | [»] | 0.285 |
| 3GXN | X-ray | 3.01 | A/B | 32-429 | [»] | [»] | 0.239 |
| 3GXP | X-ray | 2.20 | A/B | 32-429 | [»] | [»] | 0.204 |
| 3GXT | X-ray | 2.70 | A/B | 32-429 | [»] | [»] | 0.245 |
| 3HG2 | X-ray | 2.30 | A/B | 32-429 | [»] | [»] | 0.178 |
| 3HG3 | X-ray | 1.90 | A/B | 32-429 | [»] | [»] | 0.167 |
| 3HG4 | X-ray | 2.30 | A/B | 32-429 | [»] | [»] | 0.166 |
| 3HG5 | X-ray | 2.30 | A/B | 32-429 | [»] | [»] | 0.192 |
| 3LX9 | X-ray | 2.04 | A/B | 32-429 | [»] | [»] | 0.178 |
| 3LXA | X-ray | 3.04 | A/B | 32-429 | [»] | [»] | 0.216 |
| 3LXB | X-ray | 2.85 | A/B | 32-429 | [»] | [»] | 0.227 |
| 3LXC | X-ray | 2.35 | A/B | 32-429 | [»] | [»] | 0.186 |
| 3S5Y | X-ray | 2.10 | A/B | 32-429 | [»] | [»] | 0.195 |
| 3S5Z | X-ray | 2.00 | A/B | 32-429 | [»] | [»] | 0.211 |
| 3TV8 | X-ray | 2.64 | A/B | 32-429 | [»] | [»] | 0.203 |
</figtable>
We chose to use the structure 3HG3, since it has the best resolution (1.90 Å) and the second best R-factor (see <xr id="tab:Prep"/>). The best R-factor, which is a measure of the agreement between the crystallographic model and the experimental X-ray diffraction data <ref>R-factor (crystallography) (May 17, 2012) http://en.wikipedia.org/wiki/R-factor_%28crystallography%29, June 20, 2012</ref>, could be achieved with the structure 3HG4, but it has a resolution of 2.30 Å and hence we decided to use 3HG3. All structures cover the protein completely except for the signal peptide from position 1 to 31.
Vizualisation
Map all the 10 mutations onto the crystal structure.
Create mutation
SCWRL
