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Crystal structure of CSF1R in complex with vimseltinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I1M PDB ENTRY 2I1M CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 CSF1R at 4mg/ml with 0.5mM vimseltinib: Crystallization: 100mM Tris base / HCl pH 7.71, 18% PEG 8000, 100mM MgCl2: Cryo: 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.25 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.87 α = 90 b = 61.87 β = 90 c = 181.75 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 RAYONIX MX-300 2016-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.8 45.44 99.3 0.128 0.139 0.996 10.94 6.4 9256 45.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.877 100 0.534 0.047 0.998 3.23 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2I1M CHAIN A 2.8 45.44 1.35 9224 889 98.9 0.229 0.226 0.2275 0.256 0.2574 RANDOM, 0 53.81
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 16.902 f_angle_d 0.584 f_chiral_restr 0.044 f_plane_restr 0.006 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2157 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction