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KRas-G12D-GMPPnP in complex with the nanobody KM12-AM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LRW experimental model PDB 5LZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 30% PEG 1000, 0.2 M LiNO3
Crystal Properties Matthews coefficient Solvent content 1.99 38.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.072 α = 90 b = 122.32 β = 90 c = 105.615 γ = 90
Symmetry Space Group C 2 2 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 2019-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000043 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.76 61.16 94.1 0.078 14.3 10.1 43995
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.88 56.4 1.57 1.4 12.3
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 1AKNG 2.1 24.73 31891 1638 99.3 0.241 0.2391 0.2356 0.2773 0.2736 RANDOM 43.15
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] -0.8764 2.7482 -1.8718
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.73 t_omega_torsion 3.12 t_angle_deg 0.93 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4189 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 66
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing