☰ Navigation Tabs
Crystal Structure of small molecule KN2H covalently bound to K-Ras(G12D)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RPZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.06M citric acid, 0.04M bis-tris propane, pH 4.1, 16% w/v peg3350
Crystal Properties Matthews coefficient Solvent content 2.45 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.099 α = 90 b = 51.955 β = 90 c = 90.475 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 PILATUS3 6M 2023-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97852 SSRF BL19U1
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 1.72 50 99.8 0.115 0.121 0.036 0.995 7.2 11.9 21135
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 1.72 1.78 98.7 0.561 0.593 0.191 0.895 9.3
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.72 25.98 1.38 20679 1083 99.67 0.1934 0.1924 0.1927 0.2115 0.2112
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 21.834 f_angle_d 1.204 f_chiral_restr 0.059 f_bond_d 0.009 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1347 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data scaling HKL-3000 data reduction PHASER phasing