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Crystal structure of p53 cancer mutant Y220N
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SHZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 22.5% (w/v) BMW PEG smear broad, 0.1 M potassium sodium tartrate, 10% (w/v) ethylene glycol, 0.1 M sodium cacodylate, pH 5.3-5.8
Crystal Properties Matthews coefficient Solvent content 2.47 50.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.055 α = 90 b = 71.019 β = 90 c = 104.826 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 EIGER X 16M 2020-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999987 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 47.97 98.4 0.084 0.998 10.2 5.5 53010 19.1613797382
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 99.4 0.938 0.768 2.1 5.6
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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.7 47.97 1.337187589 52846 2729 97.5882700547 0.187481128669 0.185178006094 0.1902 0.228646175854 0.2325 25.0158814749
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 12.9103235091 f_angle_d 0.753983594198 f_chiral_restr 0.0522156882512 f_plane_restr 0.0055772146154 f_bond_d 0.00529216557993
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3020 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 22
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing