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Crystal structure of p53 Y220C mutant in complex with PC-9859
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 p53, at 6.93mg/ml; Optimization screen PMV1-opt1 e2: 18% PEG 8000, 20% glycerol, 20mM K2HPO4; protein + 1mM compound PC-8959; cryo: direct; crystal tracking ID 272674 e2, puck mqj6-10
Crystal Properties Matthews coefficient Solvent content 2.44 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.72 α = 90 b = 70.98 β = 90 c = 104.9 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 CCD RAYONIX MX-300 2016-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.7 47.824 99.7 0.071 0.077 0.999 18.27 5.919 53800 14.271
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 97.3 0.481 0.547 0.859 3.43 4.301
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1.7 47.82 1.35 53719 1998 99.68 0.1549 0.1541 0.1545 0.1747 0.1747 0 20.1719
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.858 f_angle_d 0.893 f_chiral_restr 0.056 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3033 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 78
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHENIX phasing