Difference between revisions of "Gaucher Disease: Task 09 - Lab Journal"
From Bioinformatikpedia
Kalemanovm (talk | contribs) (Created page with "'''This page is under construction.''' ==Preparation== ===1. Choose a structure to work with=== ===2. Visualise the mutations you want to work with=== ===3. Create mutated …") |
Kalemanovm (talk | contribs) (→1. Choose a structure to work with) |
||
Line 4: | Line 4: | ||
===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. |
||
+ | |||
+ | {| |
||
+ | !PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH || Temperature (Kelvin) |
||
+ | |- |
||
+ | |1OGS || 2.0 || A-/B || 40-536 || no || 0.195(obs.) || 0.230 || 4.60 || 100.0 |
||
+ | |- |
||
+ | |PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH |
||
+ | |- |
||
+ | |PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH |
||
+ | |- |
||
+ | |PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH |
||
+ | |- |
||
+ | |PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH |
||
+ | |} |
||
===2. Visualise the mutations you want to work with=== |
===2. Visualise the mutations you want to work with=== |
Revision as of 13:00, 28 August 2013
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 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.
PDB-ID | Resolution (Å) | Chain | Positions | Gaps | R-factor | R-free | pH | Temperature (Kelvin) |
---|---|---|---|---|---|---|---|---|
1OGS | 2.0 | A-/B | 40-536 | no | 0.195(obs.) | 0.230 | 4.60 | 100.0 |
PDB-ID | Resolution (Å) | Chain | Positions | Gaps | R-factor | R-free | pH | |
PDB-ID | Resolution (Å) | Chain | Positions | Gaps | R-factor | R-free | pH | |
PDB-ID | Resolution (Å) | Chain | Positions | Gaps | R-factor | R-free | pH | |
PDB-ID | Resolution (Å) | Chain | Positions | Gaps | R-factor | R-free | pH |