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G13D mutant of KRAS4b (2-169) bound to GDP with the switch-I in fully open conformation crystallized in sodium potassium phosphate buffer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BLR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.4 M Na/K Phosphate pH around 8.8
OR
0.9 M Na/K Phosphate pH 9.1 (sodium potassium phosphate), 0.5 M Na/K Phosphate pH 8.3
Crystal Properties Matthews coefficient Solvent content 2.43 49.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.413 α = 90 b = 76.413 β = 90 c = 55.862 γ = 120
Symmetry Space Group P 3 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 293 PIXEL DECTRIS EIGER X 16M 2022-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976254 MAX IV BioMAX
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 2.001 42.686 73.3 0.172 0.182 0.059 0.999 8.6 9.7 9569
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 2.001 2.146 1.155 1.222 0.394 0.775 2.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 42.72 9087 481 73.25 0.18288 0.17949 0.24809 0.2498 RANDOM 29.579
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] 0.19 0.1 0.19 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.5 r_long_range_B_refined 9.552 r_long_range_B_other 9.45 r_dihedral_angle_2_deg 6.885 r_dihedral_angle_1_deg 6.128 r_scangle_other 6.031 r_mcangle_it 4.219 r_mcangle_other 4.218 r_scbond_other 3.714 r_scbond_it 3.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.5 r_long_range_B_refined 9.552 r_long_range_B_other 9.45 r_dihedral_angle_2_deg 6.885 r_dihedral_angle_1_deg 6.128 r_scangle_other 6.031 r_mcangle_it 4.219 r_mcangle_other 4.218 r_scbond_other 3.714 r_scbond_it 3.71 r_mcbond_it 2.691 r_mcbond_other 2.684 r_angle_refined_deg 1.453 r_angle_other_deg 0.497 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1358 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement STARANISO data scaling XDS data reduction PHASER phasing