7THC
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B25
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 | 2020-10-29 |
| Detector | DECTRIS EIGER X 9M |
| Wavelength(s) | 0.92011 |
| Spacegroup name | P 2 21 21 |
| Unit cell lengths | 38.564, 67.190, 69.580 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 25.830 - 1.570 |
| R-factor | 0.1369 |
| Rwork | 0.134 |
| R-free | 0.16350 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 2bit |
| RMSD bond length | 0.007 |
| RMSD bond angle | 1.062 |
| 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] | 25.830 | 1.610 |
| High resolution limit [Å] | 1.570 | 1.570 |
| Rmerge | 0.056 | 0.035 |
| Rmeas | 0.020 | 0.065 |
| Rpim | 0.014 | 0.046 |
| Number of reflections | 18407 | 161 |
| <I/σ(I)> | 33.7 | |
| Completeness [%] | 71.1 | 8.7 |
| Redundancy | 10.7 | 1 |
| CC(1/2) | 0.998 | 0.963 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8 | 298 | 13% PEG 3350 0.5 M KH2PO4 7.5% glycerol Protein and inhibitor were mixed in ratio 1:2 1 uL of protein:inhibitor complex was mixed with 1 uL mother liquor |
