☰ Navigation Tabs
cocrystal structure of p53 in complex of B23
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GGB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.1M Tris pH 8.5, 10% w/v PEG3350 and 0.2M Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.93 α = 90 b = 71.8 β = 90 c = 84.62 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 S 6M 2022-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 53.44 97.4 0.154 6.2 4.6 54521
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 2.05 98.8 0.929 1.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 53.44 51846 2655 97.34 0.20172 0.20056 0.1979 0.22288 0.2097 RANDOM 36.179
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] -32.31 1.85 58.43 -26.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.938 r_dihedral_angle_4_deg 15.705 r_dihedral_angle_3_deg 15.275 r_dihedral_angle_1_deg 7.368 r_long_range_B_refined 2.461 r_long_range_B_other 2.452 r_angle_refined_deg 1.436 r_angle_other_deg 1.189 r_mcangle_it 1.183 r_mcangle_other 1.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.938 r_dihedral_angle_4_deg 15.705 r_dihedral_angle_3_deg 15.275 r_dihedral_angle_1_deg 7.368 r_long_range_B_refined 2.461 r_long_range_B_other 2.452 r_angle_refined_deg 1.436 r_angle_other_deg 1.189 r_mcangle_it 1.183 r_mcangle_other 1.182 r_scangle_other 0.972 r_mcbond_it 0.709 r_mcbond_other 0.709 r_scbond_it 0.611 r_scbond_other 0.611 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 6046 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction