5SDR
PanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z1273312153
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 | 2019-08-01 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.91589 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 101.326, 116.924, 148.068 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 91.760 - 2.077 |
R-factor | 0.2114 |
Rwork | 0.210 |
R-free | 0.23750 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 5jwf |
RMSD bond length | 0.008 |
RMSD bond angle | 0.940 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | BUSTER (2.10.3 (18-SEP-2020)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 91.763 | 91.763 | 2.268 |
High resolution limit [Å] | 2.077 | 6.524 | 2.077 |
Rmeas | 0.089 | 0.033 | 1.029 |
Rpim | 0.035 | 0.013 | 0.430 |
Total number of observations | 482462 | 22922 | 20577 |
Number of reflections | 73739 | ||
<I/σ(I)> | 13.3 | 37.8 | 1.6 |
Completeness [%] | 93.6 | 99.7 | 71.7 |
Redundancy | 6.5 | 6.2 | 5.6 |
CC(1/2) | 0.999 | 0.999 | 0.672 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.4 | 293 | Morpheus Buffer system 1, 0.06M Divalents, 30% v/v Precipitant Mix 3 |