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Structure of p53 cancer mutant Y236C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SHZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Protein solution: 5.5-6.0 mg/ml in 25 mM HEPES (pH 7.5), 200 mM NaCl, 0.5 mM TCEP.
Reservoir buffer: 19% PEG 3350 (w/v), 5% ethylene glycol (v/v), 0.2 M Na/K tartrate.
Crystal Properties Matthews coefficient Solvent content 2.6 52.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.154 α = 90 b = 71.055 β = 90 c = 105.258 γ = 90
Symmetry Space Group P 21 21 21
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 DECTRIS EIGER X 16M 2021-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall 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 2.1 43.7 97.8 0.181 0.994 6.7 5.4 28446 22.2198046869
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 2.1 2.16 99.3 0.949 0.764 2 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS FREE R-VALUE 2.1 43.7 1.33788275285 28330 1424 97.0504607585 0.225057927431 0.222727171838 0.2261 0.268388747547 0.2692 24.2653907883
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 Key Refinement Restraint Deviation f_dihedral_angle_d 13.0149275977 f_angle_d 0.850413168526 f_chiral_restr 0.0525573078174 f_bond_d 0.00685174135403 f_plane_restr 0.00680256089209
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2993 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing