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Structure of p53 cancer mutant Y234C
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 293 Protein solution: 5.5-6.0 mg/ml in 25 mM phosphate (pH 7.5), 150 mM NaCl, 0.5 mM TCEP
Reservoir buffer: 19% PEG 4000 (w/v), 0.1 M HEPES (pH 7.0), 5 mM DTT.
Crystal Properties Matthews coefficient Solvent content 2.47 50.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.059 α = 90 b = 70.987 β = 90 c = 105.127 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 2021-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 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 1.38 47.96 99.9 0.053 0.999 17.1 6.6 100451 15.2556493864
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 1.38 1.4 99.9 0.938 0.874 2.3 6.8
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 1.38 47.96 1.33784767014 100250 5078 99.6649666458 0.152920350342 0.151588410922 0.1551 0.177960257916 0.1804 21.3206206148
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 17.4159256983 f_angle_d 0.773969894813 f_chiral_restr 0.0805969552834 f_plane_restr 0.00667514355663 f_bond_d 0.00463479562067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3029 Nucleic Acid Atoms Solvent Atoms 551 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing