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Crystal structure of HRas in complex with the Ras-binding and cysteine-rich domains of CRaf-kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G0N PDB entries 4G0N & 1FAR experimental model PDB 1FAR PDB entries 4G0N & 1FAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, 17% w/v PEG10000
Crystal Properties Matthews coefficient Solvent content 2.21 44.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.487 α = 90 b = 44.353 β = 103.945 c = 74.395 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2019-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.76 36.61 91.48 0.12 0.129 0.048 15.63 7.2 7159 43.52
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 2.766 2.865 49.27 0.758 0.819 0.308 0.795 2.08 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT NONE PDB entries 4G0N & 1FAR 2.766 36.61 1.36 7159 716 91.3 0.2162 0.211 0.2121 0.2637 0.2621 50.88
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 7.5107 f_angle_d 0.4415 f_chiral_restr 0.0401 f_plane_restr 0.0029 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2228 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing