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apo c-KIT-wt kinase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277.15 protein concentration: 6.6 mg/mL, 16% PEG8000, 20% ethylene glycole, 100 mM bicine, 30 mM NaI, 30 mM NaBr, 30 mM NaF
Crystal Properties Matthews coefficient Solvent content 1.97 37.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.28 α = 90 b = 69.32 β = 117.72 c = 56.13 γ = 90
Symmetry Space Group C 1 2 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 EIGER2 X 16M 2020-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
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 2 44.86 99.6 0.998 14.2 6.9 22876 36.26
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 2.1 0.686
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 2 44.86 1.36 22872 1144 99.94 0.206 0.2044 0.2042 0.2357 0.2359 42.55
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 12.1232 f_angle_d 0.6021 f_chiral_restr 0.0431 f_plane_restr 0.0051 f_bond_d 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2348 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 8
Software Software Software Name Purpose PDB_EXTRACT data extraction PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling Coot model building PHASER phasing