7THF
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B53
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | NSLS-II BEAMLINE 17-ID-1 |
Synchrotron site | NSLS-II |
Beamline | 17-ID-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-02-08 |
Detector | DECTRIS EIGER X 9M |
Wavelength(s) | 0.92011 |
Spacegroup name | P 2 21 21 |
Unit cell lengths | 38.492, 66.885, 68.968 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 25.680 - 1.100 |
R-factor | 0.1372 |
Rwork | 0.137 |
R-free | 0.14770 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2bit |
RMSD bond length | 0.007 |
RMSD bond angle | 1.063 |
Data reduction software | XDS |
Data scaling software | autoPROC |
Phasing software | PHASER |
Refinement software | PHENIX (1.17.1_3660) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 25.680 | 1.130 |
High resolution limit [Å] | 1.100 | 1.100 |
Rmerge | 0.180 | 0.596 |
Rmeas | 0.053 | 0.230 |
Rpim | 0.037 | 0.163 |
Number of reflections | 71217 | 4690 |
<I/σ(I)> | 9.6 | 3 |
Completeness [%] | 98.6 | 89.1 |
Redundancy | 13.1 | 11.3 |
CC(1/2) | 0.994 | 0.888 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 22.5% PEG 3350 0.5 M KH2PO4 1 mM NaCl Protein and inhibitor were mixed in ratio 1:2 1 uL of protein:inhibitor complex was mixed with 1 uL mother liquor |