7YGI
Crystal structure of p53 DBD domain in complex with azurin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 298 | 0.05M Na2HPO4+19.5% PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.87 | 57.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 144.839 | α = 90 |
b = 68.75 | β = 99.69 |
c = 83.847 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | AGILENT ATLAS CCD | 2021-06-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL02U1 | 0.987 | SSRF | BL02U1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 2.1 | 19.88 | 99.522 | 0.899 | 6.3 | 6.4 | 46000 | 18.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.1 | 2.175 | 0.984 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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) | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3KMD, 1E67 | 2.1 | 19.876 | 1.35 | 45781 | 2256 | 96.31 | 0.2158 | 0.213 | 0.21 | 0.2695 | 0.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 3.404 |
f_angle_d | 0.966 |
f_chiral_restr | 0.056 |
f_bond_d | 0.009 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4968 |
Nucleic Acid Atoms | |
Solvent Atoms | 568 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
ADDREF | data reduction |
ADDREF | data scaling |
AMPLE | phasing |