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Inhibitor Bound to A DFG-Out structure of the Kinase Domain of CSF-1R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 11 mg/mL protein incubated with 4 mM inhibitor at 4C overnight followed by addition of 1 ug Arg-C (per 50 ul sample) at 22C for 24 hours, followed by addition of 0.5 uL of 5 mg/mL leupeptin, followed by mixing with equal volumes of well solution:22.5-35% PEG 4000, 0.1M Tris-HCL pH 8.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.51 50.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.916 α = 90 b = 62.916 β = 90 c = 183.943 γ = 90
Symmetry Space Group P 43 21 2
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 MARMOSAIC 300 mm CCD 2009-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07816 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 3.4 20 95.2 0.156 8 3.2 5300 5285 -3 68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.4 3.52 98.5 0.579 1.9 3.3 536
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3.4 19.9 -3 5300 5035 250 95.59 0.247 0.24721 0.24518 0.2423 0.28882 0.273 RANDOM 62.589
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] 1.2 1.2 -2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.017 r_dihedral_angle_4_deg 15.613 r_dihedral_angle_3_deg 12.463 r_dihedral_angle_1_deg 4.163 r_angle_other_deg 0.721 r_angle_refined_deg 0.713 r_scangle_it 0.128 r_mcangle_it 0.072 r_scbond_it 0.072 r_chiral_restr 0.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.017 r_dihedral_angle_4_deg 15.613 r_dihedral_angle_3_deg 12.463 r_dihedral_angle_1_deg 4.163 r_angle_other_deg 0.721 r_angle_refined_deg 0.713 r_scangle_it 0.128 r_mcangle_it 0.072 r_scbond_it 0.072 r_chiral_restr 0.041 r_mcbond_it 0.038 r_bond_refined_d 0.004 r_mcbond_other 0.004 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2252 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 33
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing