7DHF
Vibrio vulnificus Wzb in complex with benzylphosphonate
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL18U1 |
Synchrotron site | SSRF |
Beamline | BL18U1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-07-18 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.9792 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 60.972, 68.304, 132.959 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.715 - 1.211 |
R-factor | 0.1447 |
Rwork | 0.143 |
R-free | 0.16920 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2wmy |
RMSD bond length | 0.002 |
RMSD bond angle | 0.589 |
Data reduction software | XDS (Jan 31, 2020 (BUILT 20200417)) |
Data scaling software | Aimless (0.5.29) |
Phasing software | PHASER (2.7.17) |
Refinement software | PHENIX (1.10.1_2155) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 66.480 | 1.232 |
High resolution limit [Å] | 1.211 | 1.211 |
Rmeas | 0.081 | 1.118 |
Rpim | 0.022 | 0.297 |
Number of reflections | 161631 | 7689 |
<I/σ(I)> | 17.9 | 2.2 |
Completeness [%] | 95.7 | 92.6 |
Redundancy | 13.6 | 13.9 |
CC(1/2) | 0.999 | 0.933 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Complex crystals were grown in drops containing 1.5 ul of protein solution (14 mg/ml protein in the buffer 10 mM HEPES, 30 mM benzylphophonate, 150 mM NaCl, 1 mM DTT, pH 7.5) and 1.5 ul of reservoir solution (100 mM HEPES pH 7.0, 25% (w/v) PEG3350). The phosphate source was not defined, which was assumed to originate from the degradation or contamination of benzylphosphonate. |