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Crystal structure of TP53 (89-293, Y220C) bound to compound 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M ammonium sulfate, 25 %w/v PEG 3350, 0.1 M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.2 44.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.49 α = 90 b = 68.54 β = 99.276 c = 59.6 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 2022-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
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 2.39 44.66 99.9 0.996 10.7 6.8 16019
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.48 0.892 1.062 0.57
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.39 44.66 16003 816 99.913 0.224 0.2201 0.2245 0.2991 0.2997 55.869
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] 2.881 4.483 -4.465 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.677 r_dihedral_angle_4_deg 19.017 r_dihedral_angle_3_deg 18.154 r_lrange_other 9.238 r_lrange_it 9.234 r_dihedral_angle_1_deg 8.025 r_scangle_it 6.85 r_scangle_other 6.848 r_mcangle_it 6.503 r_mcangle_other 6.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.677 r_dihedral_angle_4_deg 19.017 r_dihedral_angle_3_deg 18.154 r_lrange_other 9.238 r_lrange_it 9.234 r_dihedral_angle_1_deg 8.025 r_scangle_it 6.85 r_scangle_other 6.848 r_mcangle_it 6.503 r_mcangle_other 6.502 r_scbond_it 4.786 r_scbond_other 4.785 r_mcbond_other 4.566 r_mcbond_it 4.565 r_angle_refined_deg 1.283 r_angle_other_deg 1.09 r_symmetry_nbd_other 0.196 r_nbd_refined 0.188 r_symmetry_xyhbond_nbd_refined 0.18 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.16 r_symmetry_nbd_refined 0.155 r_nbd_other 0.149 r_ncsr_local_group_1 0.128 r_metal_ion_refined 0.088 r_symmetry_xyhbond_nbd_other 0.081 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.047 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3111 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing