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The Crystal Structure of p53 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GGC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.04M Potassium phosphate monobasic, 16% w/v PEG 8000, 20% v/v Glycerol
Crystal Properties Matthews coefficient Solvent content 2.48 50.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.195 α = 90 b = 70.889 β = 90 c = 105.406 γ = 90
Symmetry Space Group P 21 21 21
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 2022-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
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 1.85 47.99 99.5 0.1 10.7 5.2 42141
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 1.85 1.89 0.651
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 1.85 43.712 42101 2117 99.225 0.176 0.1745 0.1849 0.2081 0.2207 19.347
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] 1.453 -1.509 0.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.701 r_dihedral_angle_3_deg 13.915 r_dihedral_angle_other_3_deg 12.969 r_dihedral_angle_2_deg 7.888 r_lrange_it 7.128 r_lrange_other 7.003 r_dihedral_angle_1_deg 6.95 r_scangle_it 4.972 r_scangle_other 4.971 r_scbond_it 3.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.701 r_dihedral_angle_3_deg 13.915 r_dihedral_angle_other_3_deg 12.969 r_dihedral_angle_2_deg 7.888 r_lrange_it 7.128 r_lrange_other 7.003 r_dihedral_angle_1_deg 6.95 r_scangle_it 4.972 r_scangle_other 4.971 r_scbond_it 3.212 r_scbond_other 3.212 r_mcangle_other 3.198 r_mcangle_it 3.197 r_mcbond_it 2.107 r_mcbond_other 2.098 r_angle_refined_deg 1.57 r_angle_other_deg 0.53 r_symmetry_nbd_refined 0.239 r_nbd_other 0.22 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.196 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.169 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_1 0.086 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3108 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing