7KF3
Crystal structure of GDP-mannose 4,6-dehydratase from Brucella abortus (strain 2308) in complex with Guanosine-diphosphate-rhamnose
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 | 2019-12-12 |
Detector | RAYONIX MX-300 |
Wavelength(s) | 0.97872 |
Spacegroup name | P 1 |
Unit cell lengths | 59.130, 93.300, 93.770 |
Unit cell angles | 89.06, 78.91, 87.51 |
Refinement procedure
Resolution | 48.350 - 2.350 |
R-factor | 0.1751 |
Rwork | 0.174 |
R-free | 0.21010 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5uzh |
RMSD bond length | 0.005 |
RMSD bond angle | 0.747 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | MoRDa |
Refinement software | PHENIX (1.19.1) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 48.350 | 48.350 | 2.410 |
High resolution limit [Å] | 2.350 | 10.510 | 2.350 |
Rmerge | 0.047 | 0.020 | 0.418 |
Rmeas | 0.064 | 0.028 | 0.562 |
Total number of observations | 172882 | ||
Number of reflections | 78643 | 840 | 5778 |
<I/σ(I)> | 12.13 | 32.53 | 2.01 |
Completeness [%] | 96.1 | 91.7 | 96.1 |
Redundancy | 2.198 | 2.114 | 2.211 |
CC(1/2) | 0.998 | 0.998 | 0.808 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 287 | Microlytic Morpheus screen D12: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM of each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol: 100mM bicine/Trizma base pH 8.5: Braba.00085.a.AE1.PW38674 at 29.4mg/ml: tray 311690 d12: cryo: direct: puck zdr6-4. |