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Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt precursor
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 293 Protein solution: 6 mg/ml protein in 25 mm sodium phosphate, pH 7.2, 150 mM KCl, 5 mM DTT. Reservoir buffer: 100 mM Hepes, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mM DTT. Soaking buffer: 19 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 KCl.
Crystal Properties Matthews coefficient Solvent content 2.46 49.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.766 α = 90 b = 71.245 β = 90 c = 104.588 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 2020-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999977 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 1.3 47.9 99.9 0.051 1 17.7 6.6 99954 15.5601879377
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 1.38 1.4 100 0.945 0.783 2.1 6.8
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 1.38 47.9 1.34246051662 99811 4998 99.8459460811 0.149671068117 0.148390067536 0.1508 0.174151258199 0.1762 21.4422064485
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 17.7812004303 f_angle_d 0.789399848244 f_chiral_restr 0.0814944235648 f_plane_restr 0.00671205287757 f_bond_d 0.00475970992167
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3056 Nucleic Acid Atoms Solvent Atoms 515 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing