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Structure of c-Kit with allosteric inhibitor 3G8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 9.3 mg/mL protein in 250 mM NaCl, 25 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.5 mM TCEP, 1.2 mM 3G8, 0.1% w/w V8 protease. 800 nL of protein was mixed with 800 nL of crystallization solution (0.1 M Tris-HCl pH 9.1, 1.5 M diammonium hydrogen phosphate) and incubated over 0.4 mL crystallization solution in 24 well VDX plates. Crystals were cryo-protected with 20% v/v ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.38 48.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.614 α = 90 b = 65.614 β = 90 c = 159.004 γ = 120
Symmetry Space Group P 32 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 CCD ADSC QUANTUM 315r 2012-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 20 97.65 0.13 5.42 3.94 21244 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.27 99.81 0.8 1.6 4.05
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 2.25 25.32 17585 940 94.72 0.208 0.2045 0.2099 0.2734 0.2743 RANDOM 62.078
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] -0.94 -0.47 -0.94 3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.871 r_dihedral_angle_4_deg 23.022 r_dihedral_angle_3_deg 18.937 r_dihedral_angle_1_deg 6.868 r_angle_refined_deg 1.896 r_angle_other_deg 1.321 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.871 r_dihedral_angle_4_deg 23.022 r_dihedral_angle_3_deg 18.937 r_dihedral_angle_1_deg 6.868 r_angle_refined_deg 1.896 r_angle_other_deg 1.321 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2400 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling