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p53-Y220C Core Domain Covalently Bound to a Vinyl-Sulfone Fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8A92
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.48 50.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.103 α = 90 b = 71.05 β = 90 c = 105.27 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 2022-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 50 99.8 0.99 12.17 12.51 54253 34.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 0.66
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.7 48 1.35 54123 1506 99.52 0.1766 0.1756 0.176 0.2128 0.2133 33.7
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 13.2944 f_angle_d 1.0016 f_chiral_restr 0.0666 f_plane_restr 0.0123 f_bond_d 0.0097
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3028 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing