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Crystal structure of mutant cMET D1228N kinase domain in complex with inhibitor compound 13
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R1W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 22% PEG 3350
0.1M Bis-Tris pH6.5
Crystal Properties Matthews coefficient Solvent content 1.95 36.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.604 α = 90 b = 62.248 β = 90 c = 113.285 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 R 4M 2022-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.59 27.28 100 0.123 0.039 0.998 11 9.2 37674 12.31
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.647 0.567 0.24 0.893 2.2 5.2
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 X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.59 27.28 1.36 37663 2000 99.95 0.17 0.1686 0.1689 0.1947 0.1948 15.86
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 7.0635 f_angle_d 0.7901 f_chiral_restr 0.0513 f_plane_restr 0.0072 f_bond_d 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2263 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement PHENIX refinement CrysalisPro data reduction Aimless data scaling PHASER phasing