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Cocrystal structure of p53 in complex of B20
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Previously P53 structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1M Tris pH 8.5, 10% w/v PEG3350 and 0.2M Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.23 44.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.853 α = 90 b = 69.782 β = 89.97 c = 83.669 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 2020-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.978530 SSRF BL19U1
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 1.83 83.67 99.5 0.088 8.1 3.4 69672
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 1.83 1.87 99.8 0.43 2.3
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.83 83.67 64766 3558 97.52 0.21627 0.21465 0.2454 0.2145 RANDOM 21.803
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] -0.42 0.09 1.28 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.008 r_dihedral_angle_4_deg 14.174 r_dihedral_angle_3_deg 12.887 r_dihedral_angle_1_deg 6.987 r_long_range_B_refined 3.534 r_long_range_B_other 3.424 r_scangle_other 1.78 r_mcangle_it 1.689 r_mcangle_other 1.688 r_angle_refined_deg 1.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.008 r_dihedral_angle_4_deg 14.174 r_dihedral_angle_3_deg 12.887 r_dihedral_angle_1_deg 6.987 r_long_range_B_refined 3.534 r_long_range_B_other 3.424 r_scangle_other 1.78 r_mcangle_it 1.689 r_mcangle_other 1.688 r_angle_refined_deg 1.322 r_angle_other_deg 1.273 r_scbond_it 1.074 r_scbond_other 1.074 r_mcbond_it 0.981 r_mcbond_other 0.981 r_chiral_restr 0.122 r_bond_other_d 0.006 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6076 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PDB_EXTRACT data extraction PHASER phasing