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Human KRas4A (GDP) in complex with compound 16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other unreleased crystal structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 292 25% PEG 8000, 300 mM LiCl, 100 mM bis-tris propane
Crystal Properties Matthews coefficient Solvent content 2.03 39.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.065 α = 90 b = 41.054 β = 90 c = 209.005 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 2017-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97998 Diamond I03
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 1.818 209.005 99.9 0.144 0.166 0.088 0.997 10.5 6.3 29802
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 1.818 1.849 99.9 0.913 1.001 0.529 0.737 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.82 104.5 28292 1496 99.88 0.2358 0.2342 0.2422 0.2681 0.2722 RANDOM 23.757
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] 2.32 -2.41 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.353 r_dihedral_angle_4_deg 23.419 r_dihedral_angle_3_deg 14.028 r_dihedral_angle_1_deg 4.755 r_angle_other_deg 2.408 r_angle_refined_deg 2.083 r_mcangle_it 0.491 r_mcbond_it 0.277 r_mcbond_other 0.277 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.353 r_dihedral_angle_4_deg 23.419 r_dihedral_angle_3_deg 14.028 r_dihedral_angle_1_deg 4.755 r_angle_other_deg 2.408 r_angle_refined_deg 2.083 r_mcangle_it 0.491 r_mcbond_it 0.277 r_mcbond_other 0.277 r_chiral_restr 0.129 r_bond_other_d 0.035 r_bond_refined_d 0.02 r_gen_planes_other 0.019 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2689 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction