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Crystal structure of human c-KIT kinase domain in complex with AZD3229-analogue (compound 18)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HVS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 10 % PEG 4000, 20 % glycerol, 0.1 M HEPES-MOPS pH 7.5,
0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate tribasic dihydrate, 0.02 M sodium potassium tartrate tetrahydrate, 0.02 M sodium oxamate
Crystal Properties Matthews coefficient Solvent content 2.49 50.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.773 α = 90 b = 89.436 β = 90 c = 90.343 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-F 2015-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 2.33 89.44 99.5 0.125 0.992 9.6 4.7 30591 55.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.33 2.45 99.8 0.961 0.613 2.3 4.8
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 4HVS 2.33 51.28 30448 1536 99.2 0.183 0.181 0.181 0.217 0.2124 RANDOM 56.94
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] -8.0494 6.4926 1.5568
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.36 t_omega_torsion 3.3 t_angle_deg 1.05 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.36 t_omega_torsion 3.3 t_angle_deg 1.05 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 4692 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 70
Software Software Software Name Purpose BUSTER refinement xia2 data reduction Aimless data scaling PHASER phasing