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TREM2 extracellular domain (19-174) in complex with single-chain variable fragment (scFv-4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UD7 5UD7 6G8R experimental model PDB 6G8R 5UD7 6G8R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 0.2M potassium chloride, 35% pentaerythritol propoxylate 5/4,
0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 4.7 73.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.661 α = 90 b = 111.661 β = 90 c = 232.196 γ = 90
Symmetry Space Group P 41 2 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 PIXEL DECTRIS PILATUS 6M-F 2019-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 2.26 100.63 99.8 0.2129 0.218 0.999 9.96 21.4 69496 39.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.341 0.694
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 5UD7 6G8R 2.26 100.63 1.34 69496 3452 99.65 0.1924 0.1911 0.1927 0.216 0.2181 42.78
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 15.1786 f_angle_d 0.4968 f_chiral_restr 0.0407 f_plane_restr 0.0032 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5382 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 14
Software Software Software Name Purpose PHASER phasing PHENIX refinement PHENIX data processing Coot model building xia2 data processing xia2 data reduction DIALS data scaling