6CTY
Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and malate at 2.4 A resolution
Replaces: 5V0GExperimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 19-ID |
Synchrotron site | APS |
Beamline | 19-ID |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2016-11-12 |
Detector | DECTRIS PILATUS3 X 6M |
Wavelength(s) | 0.97923, 1.28241, 1.28908 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 95.838, 112.202, 208.264 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 50.010 - 2.410 |
R-factor | 0.1613 |
Rwork | 0.159 |
R-free | 0.19790 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2eg6 |
RMSD bond length | 0.009 |
RMSD bond angle | 1.209 |
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] | 50.010 | 50.000 | 2.440 |
High resolution limit [Å] | 2.400 | 6.510 | 2.400 |
Rmerge | 0.088 | 0.036 | 0.622 |
Rmeas | 0.096 | 0.039 | 0.680 |
Rpim | 0.037 | 0.015 | 0.265 |
Number of reflections | 81980 | 4625 | 4079 |
<I/σ(I)> | 7.5 | 2.1 | |
Completeness [%] | 93.8 | 98.6 | 94.1 |
Redundancy | 6.1 | 5.9 | 6 |
CC(1/2) | 0.997 | 0.778 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 289 | 0.2 uL 10 mg/mL protein in 20 mM Tris-HCl pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP + 0.2 uL MCSG 2 condition #67 (0.15 M DL-malic acid, pH 7.0, 20% w/v PEG3350), equilibrated against 1.3 M sodium chloride solution in 96-well 3-drop crystallization plate (Swissci) |