6TUD
Crystal structure of Y. pestis penicillin-binding protein 3
This is a non-PDB format compatible entry.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I04-1 |
Synchrotron site | Diamond |
Beamline | I04-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-01-17 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.9196 |
Spacegroup name | P 41 21 2 |
Unit cell lengths | 100.800, 100.800, 314.409 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.640 - 3.000 |
Rwork | 0.244 |
R-free | 0.27640 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6syn |
RMSD bond length | 0.002 |
RMSD bond angle | 1.197 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 29.640 | 3.150 |
High resolution limit [Å] | 3.000 | 3.000 |
Rmerge | 0.200 | 1.099 |
Rpim | 0.071 | 0.518 |
Number of reflections | 33546 | 4365 |
<I/σ(I)> | 9.1 | 1.4 |
Completeness [%] | 99.9 | 100 |
Redundancy | 10 | |
CC(1/2) | 0.997 | 0.941 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 296 | 1 uL of protein (in 20 mM Tris-HCl pH 7.5 150 mM NaCl and 2 mM carbenicillin) at 7 mg/ml and 0.2 uL of precipitant (0.2 M magnesium acetate, 6% gamma-PGA (Na+ form, LM) and 6% PEG8000) Crystals were then dehydrated by replacing 50% of the reservoir solution with 50% PEG10000 |