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Human p53 core domain with hot spot mutation R282W in complex with the natural CDKN1A(p21) p53-response element and Arsenic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M Sodium acetate, 0.1 M HEPES pH 8.0, 10% w/v PEG 4000, 2mM EDTA and 2mM As2O3
Crystal Properties Matthews coefficient Solvent content 3.14 60.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.815 α = 89.62 b = 95.575 β = 89.85 c = 99.646 γ = 75.79
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 9M 2018-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.03314 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.88 46.32 89.4 0.092 0.107 0.055 0.997 8.5 3.8 52345
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.99 90.1 0.576 0.667 0.336 0.931 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2J1Y 2.9 45.39 47968 2623 84.82 0.2353 0.2337 0.2246 0.2643 0.2529 RANDOM 82.75
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] -86.45 21.77 -7.02 -60.64 9.07 147.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.647 r_dihedral_angle_4_deg 19.479 r_dihedral_angle_3_deg 16.376 r_dihedral_angle_1_deg 6.458 r_angle_refined_deg 1.481 r_angle_other_deg 1.481 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.647 r_dihedral_angle_4_deg 19.479 r_dihedral_angle_3_deg 16.376 r_dihedral_angle_1_deg 6.458 r_angle_refined_deg 1.481 r_angle_other_deg 1.481 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12482 Nucleic Acid Atoms 2460 Solvent Atoms 16 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing