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p53 cancer mutant V272M in complex with DARPin C10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RCI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein solution: 0.9 mg/ml p53-DARPin complex in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP. Reservoir buffer: 2.4 M sodium malonate. Drop volume ratio 2:1.
Crystal Properties Matthews coefficient Solvent content 2.48 50.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.041 α = 90 b = 93.877 β = 109.747 c = 53.552 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 EIGER X 16M 2023-09-09 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 2.2 46.94 99.7 0.135 0.995 8.6 5.1 17985 31.15
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 2.2 2.27 99.8 0.901 0.706 2 5.2
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 2.2 46.94 1.37340082868 17953 896 99.6503108348 0.17743058057 0.175100516455 0.1763 0.222426122 0.2258 33.5778262534
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 12.5003155674 f_angle_d 0.825160970341 f_chiral_restr 0.0509496244251 f_bond_d 0.00747017184589 f_plane_restr 0.00536866985504
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2429 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing