7B1Z
Virulence-associated protein VapB from the intracellular pathogen Rhodococcus equi
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) |
Synchrotron site | PETRA III, EMBL c/o DESY |
Beamline | P14 (MX2) |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2012-10-05 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 1.23953 |
Spacegroup name | C 2 2 21 |
Unit cell lengths | 56.940, 65.340, 124.260 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 42.930 - 1.710 |
R-factor | 0.1553 |
Rwork | 0.154 |
R-free | 0.18160 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4cv7 |
RMSD bond length | 0.009 |
RMSD bond angle | 0.910 |
Data reduction software | XDS (Mar 15, 2019) |
Data scaling software | XSCALE (Jan 31, 2020) |
Phasing software | PHASER |
Refinement software | PHENIX (dev_3965) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 1.750 |
High resolution limit [Å] | 1.710 | 1.710 |
Rmeas | 0.039 | 0.657 |
Number of reflections | 25467 | 1845 |
<I/σ(I)> | 28.74 | 2.8 |
Completeness [%] | 99.8 | 99.3 |
Redundancy | 7 | 4.6 |
CC(1/2) | 1.000 | 0.850 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 14% PEG 4000, 0.2 M Mg(NO3)2; protein concentration: 10 mg/ml; protein buffer: 25 mM Tris, pH 7.0, 20 mM NaCl; drop size and ratio: 1 ul protein + 0.5 ul reservoir |