6ZI0
Crystal structure of the isolated H. influenzae VapD toxin (wildtype)
This is a non-PDB format compatible entry.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) |
Synchrotron site | PETRA III, EMBL c/o DESY |
Beamline | P13 (MX1) |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-03-22 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.98021 |
Spacegroup name | P 63 2 2 |
Unit cell lengths | 99.100, 99.100, 44.470 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 85.882 - 2.500 |
Rwork | 0.220 |
R-free | 0.26360 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6HKD |
RMSD bond length | 0.008 |
RMSD bond angle | 1.741 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0253) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 85.882 | 85.882 | 2.560 |
High resolution limit [Å] | 2.500 | 11.180 | 2.500 |
Rmerge | 0.212 | 0.036 | 1.581 |
Rmeas | 0.223 | 0.038 | 1.659 |
Number of reflections | 4800 | 74 | 344 |
<I/σ(I)> | 9.49 | 29.4 | 1.33 |
Completeness [%] | 99.9 | 98.7 | 100 |
Redundancy | 10.357 | 7.189 | 10.677 |
CC(1/2) | 0.996 | 1.000 | 0.546 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 4 | 292 | 1 M LiCl, 0.1 M citrate, 20% PEG 6000 |