8T1Z
Crystal Structure of Porphyromonas gingivalis Sialidase (PG_0352) Bound to Neu5Ac (NANA)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 23-ID-D |
Synchrotron site | APS |
Beamline | 23-ID-D |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2023-03-18 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 1.0333 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 61.255, 56.782, 80.378 |
Unit cell angles | 90.00, 96.07, 90.00 |
Refinement procedure
Resolution | 41.530 - 1.930 |
R-factor | 0.1758 |
Rwork | 0.174 |
R-free | 0.21660 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 8feb |
RMSD bond length | 0.008 |
RMSD bond angle | 0.992 |
Data reduction software | DIALS (3.8) |
Data scaling software | xia2 (3.8.6) |
Phasing software | PHASER (2.8.2) |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 41.530 | 1.999 |
High resolution limit [Å] | 1.930 | 1.930 |
Rmerge | 0.129 | 0.791 |
Rmeas | 0.157 | 0.966 |
Rpim | 0.088 | 0.547 |
Number of reflections | 40836 | 3885 |
<I/σ(I)> | 7.52 | |
Completeness [%] | 98.2 | 94.43 |
Redundancy | 3 | 2.9 |
CC(1/2) | 0.986 | 0.556 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 296 | 1.6 M ammonium citrate tribasic, pH 7.0 |