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Structure of CSF1R in complex with a pyrollopyrimidine (compound 23)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I1M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.3 M DL-Malic acid pH 7.0, 23.0% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.013 α = 90 b = 81.013 β = 90 c = 143.237 γ = 120
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 PILATUS 6M 2018-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.99187 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.925 31.895 97.6 0.061 0.071 0.036 0.997 10.7 3.6 25909 28.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.925 1.994 98.2 0.451 0.536 0.282 0.89 2.6 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 2i1m 1.925 31.895 25909 1231 97.56 0.154 0.1516 0.1613 0.2059 0.212 32.398
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] -1.17 -0.585 -1.17 3.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.568 r_dihedral_angle_3_deg 15.022 r_lrange_it 9.311 r_lrange_other 9.188 r_dihedral_angle_2_deg 8.115 r_dihedral_angle_1_deg 6.86 r_scangle_it 6.507 r_scangle_other 6.506 r_mcangle_other 5.164 r_mcangle_it 5.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.568 r_dihedral_angle_3_deg 15.022 r_lrange_it 9.311 r_lrange_other 9.188 r_dihedral_angle_2_deg 8.115 r_dihedral_angle_1_deg 6.86 r_scangle_it 6.507 r_scangle_other 6.506 r_mcangle_other 5.164 r_mcangle_it 5.163 r_scbond_it 4.023 r_scbond_other 4.021 r_mcbond_it 3.364 r_mcbond_other 3.364 r_angle_refined_deg 1.38 r_angle_other_deg 0.495 r_symmetry_nbd_refined 0.265 r_nbd_refined 0.221 r_nbd_other 0.208 r_xyhbond_nbd_refined 0.207 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.186 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2462 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling REFMAC phasing