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Crystal structure of the kinase domain of human c-KIT in complex with a type-II inhibitor bearing an acrylamide
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 7.5 293 10 % PEG4000, 20 % glycerol, 10 % MORPHEUS carboxylic acids, 0.1 M HEPES-MOPS buffer pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.41 48.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.135 α = 90 b = 90.045 β = 90 c = 90.745 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 PILATUS 6M 2015-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97858 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.297 45.37 93.7 0.13 0.145 0.063 0.997 9.8 5.1 22158 51.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.297 2.48 82.7 1.101 1.2 0.471 0.7 6.3
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 2.3 44.068 22141 1144 67.3 0.198 0.196 0.1996 0.245 0.2427 RANDOM 51.86
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] 3.9504 1.8109 -5.7613
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.77 t_omega_torsion 2.93 t_angle_deg 1.13 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 18.77 t_omega_torsion 2.93 t_angle_deg 1.13 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 4600 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 76
Software Software Software Name Purpose XDS data reduction Aimless data scaling AMoRE phasing BUSTER refinement PDB_EXTRACT data extraction