8A31
p53 cancer mutant Y220C in complex with iodophenol-based small-molecule stabilizer JC694
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6SHZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Protein solution: 5.7 mg/ml protein in 25 mM sodium phosphate, pH 7.2, 150 mm NaCl, 0.5 mM TCEP. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 20 mM compound in 100 mm HEPES, pH 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm NaCl. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.981 | α = 90 |
b = 71.063 | β = 90 |
c = 105.089 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | PIXEL | DECTRIS EIGER X 16M | 2020-12-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.999998 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.46 | 49.5 | 99.2 | 0.062 | 0.999 | 12.9 | 5.6 | 84274 | 14.3992113092 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.46 | 1.48 | 98.2 | 0.821 | 0.911 | 2.3 | 5.8 |
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 | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | FREE R-VALUE | 6shz | 1.46 | 47.9807 | 1.33787302829 | 84099 | 4200 | 98.8434822467 | 0.158944359505 | 0.157258724081 | 0.190642504555 | 21.1746285667 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.5779014629 |
f_angle_d | 0.878061384113 |
f_chiral_restr | 0.0845719654955 |
f_plane_restr | 0.00696013630109 |
f_bond_d | 0.0065403639898 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3033 |
Nucleic Acid Atoms | |
Solvent Atoms | 434 |
Heterogen Atoms | 44 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
PHENIX | phasing |
PHENIX | refinement |