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Arsenic-bound p53 DNA-binding domain mutant G245S
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 Tris (pH 8.0-8.5), 20% (w/v) PEG 8000, 0.2 M Li2SO4, 2 mM EDTA, and 2 mM As2O3
Crystal Properties Matthews coefficient Solvent content 2.16 42.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.109 α = 90 b = 68.243 β = 90.03 c = 83.621 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 6M 2018-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.15 50 94.8 0.083 12.7 4.2 41923
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.22 93.3 0.26 6.6 6.6
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 2.15 48.21 37578 2007 94.39 0.1888 0.1872 0.1821 0.219 0.214 RANDOM 37.004
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] -22.7 -7.7 32.45 -9.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.018 r_dihedral_angle_3_deg 12.966 r_dihedral_angle_4_deg 11.591 r_dihedral_angle_1_deg 5.907 r_angle_refined_deg 1.304 r_angle_other_deg 1.001 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.018 r_dihedral_angle_3_deg 12.966 r_dihedral_angle_4_deg 11.591 r_dihedral_angle_1_deg 5.907 r_angle_refined_deg 1.304 r_angle_other_deg 1.001 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6114 Nucleic Acid Atoms Solvent Atoms 517 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing