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Human p53 DNA-binding domain bound to DARPin C10-H82R
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: 2.6 mg/ml p53 DBD-DARPin C10-H82R complex in
50 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM TCEP.
Reservoir solution: 0.1 M Bis-Tris propane, pH 7.5, 0.02 M sodium potassium phosphate, pH 7.5, 20% (w/v) PEG 3350, 10% (v/v) ethylene glycol.
Drop volume ratio: 2:1
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.713 α = 90 b = 94.011 β = 110.108 c = 53.17 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 2023-06-23 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) Rrim I (All) Rpim 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 1.44 47 98.9 0.045 0.053 0.027 0.999 12.5 3.8 62097 19.0208313695
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.44 1.47 97.9 0.612 0.707 0.351 0.825 2 3.9
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 1.44 47 1.34347927413 62039 3019 98.8055232604 0.155892331052 0.154445713844 0.1566 0.183968942353 0.1857 27.4562657645
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 16.2978358942 f_angle_d 0.737427751879 f_chiral_restr 0.0776390417033 f_bond_d 0.00489935990145 f_plane_restr 0.00489056704613
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2442 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing