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Structure of the human CSF-1:CSF-1R complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DKD 4DKD, 3UF2 experimental model PDB 3UF2 4DKD, 3UF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5 and 28% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.44 64.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.997 α = 90 b = 142.997 β = 90 c = 138.323 γ = 90
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 PSI PILATUS 6M 2014-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 49.71 99.8 0.064 20.73 6.9 34125 82.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.97 99.2 0.815 2.32 6.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4DKD, 3UF2 2.802 49.71 1.36 34117 1706 99.83 0.225 0.2231 0.2325 0.2613 0.2685
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 13.446 f_angle_d 1.094 f_chiral_restr 0.052 f_plane_restr 0.014 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6370 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 287
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing