8UC5
Apo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I)
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 | 2022-02-02 |
Detector | DECTRIS EIGER X 9M |
Wavelength(s) | 0.9201 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 123.667, 56.643, 101.172 |
Unit cell angles | 90.00, 123.72, 90.00 |
Refinement procedure
Resolution | 29.330 - 1.430 |
R-factor | 0.1448 |
Rwork | 0.144 |
R-free | 0.17540 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.010 |
RMSD bond angle | 1.122 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | DIMPLE |
Refinement software | PHENIX (1.18rc7_3834) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 29.330 | 1.470 |
High resolution limit [Å] | 1.430 | 1.430 |
Rmeas | 0.093 | 0.807 |
Number of reflections | 105128 | 7331 |
<I/σ(I)> | 8.8 | 1.5 |
Completeness [%] | 97.6 | 92.3 |
Redundancy | 3.8 | 3.6 |
CC(1/2) | 0.997 | 0.657 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | Well solution: 2.1 M DL-Malic acid pH 7.0. Protein solution: 15 mg/mL protein, 20 mM Tris pH 8.0, 50 mM NaCl, 1 mM DTT, and 5% glycerol. Drop: 1 uL protein, 1 uL well solution |