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 |
