☰ Navigation Tabs
Crystal structure of p53 cancer mutant Y220S in complex with rezatapopt
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 in 25 mM Hepes, pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 1 mM Rezatapopt, 2% DMSO. Reservoir buffer: 0.2 M ammonium nitrate, 20% PEG 3350 (protein:buffer 2:1). Cryo: reservoir buffer supplemented with 23% ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.45 49.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.78 α = 90 b = 70.991 β = 90 c = 104.645 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 2024-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
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 1.4 55.1 99.5 0.066 0.999 16.2 9.4 95141 14.86
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 1.4 1.42 94 0.71 0.759 2 6.3
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 1.4 47.9 1.35017416071 94982 4852 99.4034661755 0.163011235977 0.161605367045 0.1666 0.188399780399 0.1928 21.6974802549
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 14.2872196363 f_angle_d 0.789488454253 f_chiral_restr 0.0798825749381 f_plane_restr 0.00796126660718 f_bond_d 0.00472663866673
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3053 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 164
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing