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KRAS-169 Q61H GPPNHP + CH-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 8-15% w/v polyethylene glycol 3350 and 0.2M Lithium citrate
Crystal Properties Matthews coefficient Solvent content 2.49 50.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.531 α = 90 b = 118.678 β = 90 c = 156.996 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 EIGER X 16M 2017-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
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 2.75 118 99.8 0.14 0.16 0.067 0.997 16 10.5 31557
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 2.75 2.88 99.9 0.54 0.59 0.24 0.916 1.7 11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3GFT 2.75 94.67 29946 1561 99.6 0.20682 0.20476 0.2059 0.24744 0.2441 RANDOM 44.271
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] -0.41 1.78 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.928 r_dihedral_angle_3_deg 16.579 r_dihedral_angle_4_deg 12.952 r_long_range_B_refined 11.013 r_long_range_B_other 11.012 r_scangle_other 8.084 r_mcangle_it 6.103 r_mcangle_other 6.103 r_dihedral_angle_1_deg 5.577 r_scbond_other 4.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.928 r_dihedral_angle_3_deg 16.579 r_dihedral_angle_4_deg 12.952 r_long_range_B_refined 11.013 r_long_range_B_other 11.012 r_scangle_other 8.084 r_mcangle_it 6.103 r_mcangle_other 6.103 r_dihedral_angle_1_deg 5.577 r_scbond_other 4.936 r_scbond_it 4.935 r_mcbond_it 3.711 r_mcbond_other 3.711 r_angle_refined_deg 1.502 r_angle_other_deg 0.797 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7940 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 310
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing