3QXX
Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GDP and 8-aminocaprylic acid
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 19-BM |
Synchrotron site | APS |
Beamline | 19-BM |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2008-07-11 |
Detector | SBC-3 |
Wavelength(s) | 0.9793 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 81.883, 37.845, 68.839 |
Unit cell angles | 90.00, 101.30, 90.00 |
Refinement procedure
Resolution | 50.000 - 1.360 |
R-factor | 0.13125 |
Rwork | 0.130 |
R-free | 0.16171 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2qmo |
RMSD bond length | 0.019 |
RMSD bond angle | 1.683 |
Data reduction software | HKL-3000 |
Data scaling software | HKL-3000 |
Phasing software | HKL-3000 |
Refinement software | REFMAC (5.5) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 1.380 |
High resolution limit [Å] | 1.360 | 1.360 |
Rmerge | 0.061 | 0.386 |
Number of reflections | 43768 | |
<I/σ(I)> | 29.5 | 2.5 |
Completeness [%] | 98.1 | 86.6 |
Redundancy | 3.8 | 2.8 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 20% PEG3350; 100 MM NH4NO3; 100 MM BIS-TRIS; 5% GLYCEROL; SOAKED WITH 10 MM GDP, 10 MM MGCL2, 10 MM 8-AMINOOCTANOIC ACID; IN SITU PROTEOLYSIS - CHYMOTRYPSIN, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |