6C1Q
Crystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53 and an allosteric antagonist NDT9513727
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 23-ID-B |
Synchrotron site | APS |
Beamline | 23-ID-B |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-08-15 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 1 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 62.369, 52.558, 84.503 |
Unit cell angles | 90.00, 107.75, 90.00 |
Refinement procedure
Resolution | 29.413 - 2.900 |
R-factor | 0.244 |
Rwork | 0.242 |
R-free | 0.28570 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.004 |
RMSD bond angle | 0.779 |
Data reduction software | HKL-2000 |
Data scaling software | SCALEPACK |
Phasing software | PHASER |
Refinement software | PHENIX (1.9_1692) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 30.000 | 30.000 | 2.950 |
High resolution limit [Å] | 2.900 | 7.830 | 2.900 |
Rmerge | 0.106 | 0.057 | 0.550 |
Rmeas | 0.113 | 0.060 | 0.590 |
Rpim | 0.037 | 0.020 | 0.203 |
Number of reflections | 10290 | 581 | 418 |
<I/σ(I)> | 6.1 | ||
Completeness [%] | 85.5 | 90.4 | 68.5 |
Redundancy | 7.5 | 7.1 | 6.1 |
CC(1/2) | 0.995 | 0.870 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | LIPIDIC CUBIC PHASE | 6.5 | 283 | 25-35% PEG300, 100 mM MES, pH 6.5, 80-150 mM sodium malonate, 0.5% P400, 5 uM NDT, 5 uM PMX53 |