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Crystal structure of the kinase domain of human c-KIT with a cyclic imidate inhibitor covalently bound to Cys788
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other internal model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.2 293 9 % PEG8000, 18 % ethylene glycol, 10 % MORPHEUS halogens, 0.1 M Imidazole-MES buffer pH 6.2
Crystal Properties Matthews coefficient Solvent content 2.42 49.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.71 α = 90 b = 90.272 β = 90 c = 91.178 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 EIGER2 XE 16M 2019-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.15 63.211 92.7 0.096 0.999 9.9 6.7 35714 55.24
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 2.15 2.251 47.7 0.509 1.4
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 internal model 2.15 63.21 35714 1950 89.3 0.194 0.192 0.1971 0.223 0.2215 RANDOM 66.71
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] -3.3493 2.4448 0.9045
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.65 t_omega_torsion 3.13 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.65 t_omega_torsion 3.13 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4629 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 80
Software Software Software Name Purpose XDS data reduction Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction AMoRE phasing