4D1M
Tetramerization domain of zebrafish p53 (crystal form II)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | SITTING DROP VAPOR DIFFUSION AT 20 DEGREE C; PROTEIN SOLUTION: 12 MG/ML IN 20 MM TRIS PH 7.5, 50 MM NACL, 5 MM DTT; CRYSTALLIZATION BUFFER: 160 MM ZINC ACETATE, 80 MM SODIUM CACODYLATE, PH 6.5, 12% (W/V) POLYETHYLENE GLYCOL 8,000 AND 19% (W/V) GLYCEROL | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.6 | 53 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 70.861 | α = 90 |
| b = 74.507 | β = 117.79 |
| c = 74.945 | 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 | M | SINGLE WAVELENGTH | |||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | Diamond | I03 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.2 | 28.9 | 99.3 | 0.04 | 14.8 | 3.4 | 34925 | 2 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.2 | 2.32 | 99.5 | 0.52 | 2.5 | 3.3 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.2 | 28.9 | 33164 | 1744 | 99.24 | 0.22845 | 0.2259 | 0.23 | 0.27996 | 0.23 | RANDOM | 57.722 | |||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| 2.2 | -0.29 | -0.14 | -1.13 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.097 |
| r_dihedral_angle_4_deg | 19.387 |
| r_dihedral_angle_3_deg | 17.22 |
| r_dihedral_angle_1_deg | 4.824 |
| r_mcangle_it | 2.369 |
| r_scbond_it | 2.057 |
| r_mcbond_it | 1.626 |
| r_mcbond_other | 1.625 |
| r_angle_refined_deg | 1.336 |
| r_angle_other_deg | 0.777 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3964 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 59 |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
