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Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273H mutant bound to MQ: R273H-MQ (II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IBS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.1 292 0.2M Li Acetate, 2.0% w/v Agarose, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.46 50.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.249 α = 90 b = 72.003 β = 90.066 c = 85.233 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 2M 2016-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87290 ESRF ID23-2
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 2.05 39 94.2 0.114 0.136 0.073 0.986 10.18 3.1 49698
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 2.05 2.09 81.1 0.254 0.303 0.162 0.91 3
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 4IBS 2.05 36.67 47284 2400 93.9 0.1787 0.1762 0.1933 0.2275 0.2469 RANDOM 31.036
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] -7.59 -4.02 11 -3.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.805 r_dihedral_angle_4_deg 17.704 r_dihedral_angle_3_deg 15.253 r_dihedral_angle_1_deg 8.019 r_angle_refined_deg 2.012 r_angle_other_deg 1.44 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.805 r_dihedral_angle_4_deg 17.704 r_dihedral_angle_3_deg 15.253 r_dihedral_angle_1_deg 8.019 r_angle_refined_deg 2.012 r_angle_other_deg 1.44 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5955 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing