5UMM
CRYSTAL STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH 12-MER PEPTIDE INHIBITOR M3
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 298 | 0.1 M sodium cacodylate pH 5.5, 25% PEG (w/v) 4000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.84 | 33.2 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 26.567 | α = 90 |
| b = 87.895 | β = 92.3 |
| c = 36.576 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | PSI PILATUS 6M | 2016-11-27 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.9795 | SSRL | BL12-2 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rpim I (All) | 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 | 1.65 | 43.95 | 96.4 | 0.866 | 1.09 | 3.2 | 19635 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 3IWY | 1.65 | 43.95 | 18598 | 1012 | 96.4 | 0.18052 | 0.17795 | 0.23112 | RANDOM | 32.574 | ||||||
| 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] | |
| -1.29 | 1.19 | -1.82 | 3 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 42.183 |
| r_dihedral_angle_4_deg | 23.709 |
| r_dihedral_angle_3_deg | 16.908 |
| r_dihedral_angle_1_deg | 6.811 |
| r_long_range_B_refined | 5.766 |
| r_long_range_B_other | 5.752 |
| r_scangle_other | 4.412 |
| r_scbond_it | 2.825 |
| r_scbond_other | 2.823 |
| r_angle_refined_deg | 2.379 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1572 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 73 |
| Heterogen Atoms | 1 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PHASER | phasing |
| HKL-2000 | data scaling |
| HKL-2000 | data reduction |
