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KRAS G12D Mutant in complex with GMPPCP and cyclic peptide MP-9903
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XCO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 100mM Bis-Tris and 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.93 36.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.793 α = 90 b = 71.764 β = 100.29 c = 65.481 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M 2018-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.32 47.9 96.2 0.996 9.7 3.3 74611
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.356 0.55
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 5xco 1.32 47.94 74611 3606 90.1 0.1948 0.1937 0.1867 0.2156 0.2083 RANDOM 19.76
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] -0.0039 -0.0299 -0.1483 0.1522
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.4 t_omega_torsion 3.84 t_angle_deg 1 t_bond_d 0.009 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 2864 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 72
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction STARANISO data scaling MOLREP phasing