4ZSC
Human Cyclophilin D Complexed with an Inhibitor at room temperature
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.3 | 291 | 30% PEG4000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.1 | 41.36 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.866 | α = 90 |
| b = 57.866 | β = 90 |
| c = 88.463 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 298 | CCD | ADSC QUANTUM 315r | 2015-05-07 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.9797 | ESRF | BM30A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||||
| 1 | 1.5 | 48.4 | 73.1 | 12.1 | 2.8 | 16982 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | THROUGHOUT | 1.5 | 48.43 | 16982 | 862 | 72.05 | 0.135 | 0.1336 | 0.1628 | RANDOM | 9.817 | ||||||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| 0.02 | 0.02 | -0.04 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.012 |
| r_dihedral_angle_4_deg | 17.501 |
| r_sphericity_free | 14.002 |
| r_dihedral_angle_3_deg | 12.404 |
| r_dihedral_angle_1_deg | 5.938 |
| r_sphericity_bonded | 2.256 |
| r_angle_refined_deg | 1.3 |
| r_angle_other_deg | 0.887 |
| r_rigid_bond_restr | 0.833 |
| r_mcangle_it | 0.615 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1225 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 91 |
| Heterogen Atoms | 18 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| XSCALE | data scaling |
| Coot | model building |
| XDS | data reduction |
| REFMAC | phasing |
