3Q4D
Crystal structure of dipeptide epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Ala
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2010-06-03 |
Detector | RAYONIX MX-225 |
Wavelength(s) | 0.97872 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 94.560, 158.090, 182.180 |
Unit cell angles | 90.00, 100.04, 90.00 |
Refinement procedure
Resolution | 20.000 - 3.000 |
R-factor | 0.23106 |
Rwork | 0.230 |
R-free | 0.25388 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1tkk |
RMSD bond length | 0.009 |
RMSD bond angle | 1.009 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHASER |
Refinement software | REFMAC (5.5.0109) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 20.000 | 20.000 | 3.110 |
High resolution limit [Å] | 3.000 | 6.400 | 3.000 |
Rmerge | 0.138 | 0.030 | 0.716 |
Number of reflections | 105392 | ||
<I/σ(I)> | 11.88 | 26.93 | 2.4 |
Completeness [%] | 99.8 | 98.9 | 100 |
Redundancy | 10.3 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 4 | 277 | Precipitant contained 10% PEG 4000 and 0.1M Na-citrate. Protein solution contained 0.1M NaCl, 10% glycerol, and 0.02M D-Ala-L-Ala, Protein concentration was 40 mg/mL, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |