5VGM
Crystal structure of dihydroorotase pyrC from Vibrio cholerae in complex with zinc at 1.95 A resolution.
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 | 2017-03-12 |
Detector | MARMOSAIC 300 mm CCD |
Wavelength(s) | 0.97872 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 62.507, 57.257, 87.524 |
Unit cell angles | 90.00, 105.09, 90.00 |
Refinement procedure
Resolution | 20.000 - 1.950 |
R-factor | 0.1695 |
Rwork | 0.168 |
R-free | 0.20300 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5V0G |
RMSD bond length | 0.010 |
RMSD bond angle | 1.349 |
Data reduction software | HKL-3000 |
Data scaling software | SCALEPACK |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0158) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 20.000 | 20.000 | 1.980 |
High resolution limit [Å] | 1.950 | 5.260 | 1.950 |
Rmerge | 0.063 | 0.045 | 0.372 |
Rmeas | 0.075 | 0.053 | 0.454 |
Rpim | 0.040 | 0.028 | 0.257 |
Number of reflections | 41257 | 1353 | |
<I/σ(I)> | 11.4 | 2.3 | |
Completeness [%] | 94.1 | 95.2 | 62.5 |
Redundancy | 3.3 | 3.3 | 2.6 |
CC(1/2) | 0.870 | 0.997 | 0.871 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 289 | 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCE, and 20 mM L-citruline were mixed with 0.2 ul of the Top96 screen condition #C11 (0.2 M Sodium Acetate 0.1 M Sodium Cacodylate: HCl, pH 6.5 30 % (w/v) PEG 8000), 0.1 ul of the Hampton Additive screen # 94 (7%v/v 1-Butanol) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 1 hours. |