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Crystal structure of c-Met-D1228N in complex with KIN-7615
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1M HEPES pH7.5, 12.5% PEG4000, 10% isopropanol
Crystal Properties Matthews coefficient Solvent content 2.87 57.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.66 α = 90 b = 69.82 β = 95.84 c = 78.06 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 2022-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
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 3.11 43.83 78.3 0.105 11.7 6.8 11252
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 3.11 3.32 0.372
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.11 43.83 10751 500 78.2 0.2531 0.25112 0.252 0.29791 0.2987 RANDOM 72.851
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] 0.27 0.26 0.02 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.965 r_dihedral_angle_2_deg 4.509 r_dihedral_angle_1_deg 4.335 r_long_range_B_refined 2.314 r_long_range_B_other 2.313 r_mcangle_it 0.649 r_mcangle_other 0.649 r_angle_refined_deg 0.61 r_scangle_other 0.349 r_mcbond_it 0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.965 r_dihedral_angle_2_deg 4.509 r_dihedral_angle_1_deg 4.335 r_long_range_B_refined 2.314 r_long_range_B_other 2.313 r_mcangle_it 0.649 r_mcangle_other 0.649 r_angle_refined_deg 0.61 r_scangle_other 0.349 r_mcbond_it 0.344 r_mcbond_other 0.344 r_angle_other_deg 0.23 r_scbond_it 0.163 r_scbond_other 0.163 r_chiral_restr 0.029 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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 4545 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing