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KIT kinase domain in complex with a pyrrolopyrimidine-based compound (17)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PQ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 285.15 14% PEG3350, 100 mM tri-lithium citrate, 100 mM Tris pH 7.5; 285.15 K (cryoprotectant:ethylene glycol)
Crystal Properties Matthews coefficient Solvent content 2.24 45.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.58 α = 90 b = 58.97 β = 90 c = 192.9 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 X 9M 2024-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 48.23 99.9 0.998 10.52 13.5 62866 34.8
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 1.8 1.9 0.761
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 1.8 48.23 1.35 62844 3143 99.82 0.1846 0.183 0.1833 0.2144 0.2147 41.63
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 16.1937 f_angle_d 0.7152 f_chiral_restr 0.0475 f_plane_restr 0.0066 f_bond_d 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4701 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing