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Kras-G12D-GDP-MRTX1133 by FIB-MicroED
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RPZ
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.88 α = 90 b = 49.28 β = 90 c = 87.2 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
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B ELECTRON CRYSTALLOGRAPHY FREE R-VALUE 3 35.51 1.35 6411 651 99.18 0.3134 0.31 0.3243 0.3366 0.3489 30.68
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.3004 f_angle_d 1.6433 f_chiral_restr 0.0915 f_bond_d 0.0108 f_plane_restr 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1327 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 73
Software Software Software Name Purpose PHENIX refinement
Sample Isoform 2B of GTPase KRas
GUANOSINE-5'-DIPHOSPHATE
4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)-5-ethynyl-6-fluoronaphthalen-2-ol
MAGNESIUM ION
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 39.868 Length b 51.757 Length c 51.757 Angle Alpha 90 Angle Beta 90 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 (7RPZ) Refinement Space REAL Refinement Protocol OTHER Refinement Target Correlation coefficient Overall B Value 200 Fitting Procedure Details no
Data Acquisition Detector Type DIRECT ELECTRON DE-20 (5k x 3k) Electron Dose (electrons/Å**2) 0.02
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL 2100F Minimum Defocus (nm) 1500 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode DIFFRACTION Specimen Holder Model FISCHIONE 2550 Nominal Magnification 6000 Calibrated Magnification 6000 Source LAB6 Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version MODEL FITTING Coot 0.9.4 MODEL REFINEMENT PHENIX 1.19.2 MOLECULAR REPLACEMENT PHENIX 1.19.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE