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Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt analog 7
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 mM Hepes, pH 7.0, 19% (w/v) polyethylene glycol 4000. 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 2.45 49.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.832 α = 90 b = 71.037 β = 90 c = 104.564 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 EIGER2 XE 16M 2024-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97627 Diamond I04
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 1.83 71.04 100 0.074 0.999 17.5 13.7 43365 31.95
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 1.83 1.87 100 1.622 0.895 1.9 14.1
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 1.83 55.1 1.33788785473 43169 2081 99.6583327562 0.193214583308 0.191622997646 0.1961 0.225517227347 0.2276 39.7950390633
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 10.8646570105 f_angle_d 0.804726541856 f_chiral_restr 0.0541165895335 f_plane_restr 0.00714947451178 f_bond_d 0.00646083318894
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3029 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing