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Crystal structure of TP53 (89-293, Y220C)
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 0.05 M ammonium sulfate, 15 %w/v PEG 8000, 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.22 44.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.31 α = 90 b = 68.44 β = 98.806 c = 60.12 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) 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 2.11 44.87 99.9 0.113 0.134 0.071 0.997 11 6.7 23331
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 2.11 2.17 0.83 0.988 0.526
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 2.11 44.87 23315 1173 99.91 0.205 0.2021 0.2081 0.2633 0.2656 40.347
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] 2.526 3.82 -2.763 -0.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.524 r_dihedral_angle_4_deg 17.383 r_dihedral_angle_3_deg 16.077 r_dihedral_angle_1_deg 7.955 r_lrange_it 6.624 r_lrange_other 6.618 r_scangle_it 4.79 r_scangle_other 4.787 r_mcangle_it 3.924 r_mcangle_other 3.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.524 r_dihedral_angle_4_deg 17.383 r_dihedral_angle_3_deg 16.077 r_dihedral_angle_1_deg 7.955 r_lrange_it 6.624 r_lrange_other 6.618 r_scangle_it 4.79 r_scangle_other 4.787 r_mcangle_it 3.924 r_mcangle_other 3.919 r_scbond_it 3.236 r_scbond_other 3.235 r_mcbond_it 2.722 r_mcbond_other 2.72 r_angle_refined_deg 1.2 r_angle_other_deg 1.136 r_nbd_other 0.204 r_symmetry_xyhbond_nbd_refined 0.196 r_nbd_refined 0.188 r_symmetry_nbd_other 0.188 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.152 r_symmetry_nbd_refined 0.139 r_ncsr_local_group_1 0.109 r_symmetry_nbtor_other 0.075 r_metal_ion_refined 0.065 r_chiral_restr 0.047 r_symmetry_xyhbond_nbd_other 0.046 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 3150 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing