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Crystal structure of p53 Y220C covalently bound to indole KG6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J1X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 100 mM HEPES, 2.2M MgSO4
Crystal Properties Matthews coefficient Solvent content 2.56 51.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.04 α = 90 b = 105.75 β = 90 c = 105.75 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 80 CCD ADSC QUANTUM 315r 2021-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1 ALS 8.2.1
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 1.6 57.78 99 0.999 20.3 2 133925 15.2051228967
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 1.6 1.6 0.947
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2J1X 1.60000908706 47.2928377241 1.34297848669 133895 6607 99.3721287507 0.182425826238 0.181395773567 0.184 0.202329214824 0.2039 21.5712440779
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 15.2033672751 f_angle_d 1.26336112416 f_chiral_restr 0.0631557693318 f_plane_restr 0.00835959429915 f_bond_d 0.00812842673804
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6053 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms 135
Software Software Software Name Purpose Blu-Ice data collection iMOSFLM data reduction Aimless data scaling PHASER phasing PHENIX refinement