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p53-Y220C Core Domain Covalently Bound to 5-Chloro-6-methylpyrazine-2-carbonitrile Soaked at 5 mM
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 7.2 293 100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.5 50.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.191 α = 90 b = 71.145 β = 90 c = 105.73 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 2023-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.92 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.56 50 100 0.12 0.99 13.02 12 70579 23.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.66 2.39 0.58 1.03 12.38
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 1.56 48.06 1.35 70534 1500 99.91 0.1506 0.1496 0.1686 0.1986 0.2105 30.49
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 13.1487 f_angle_d 0.8109 f_chiral_restr 0.0579 f_plane_restr 0.012 f_bond_d 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3009 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 131
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing