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TREM2 extracellular domain (19-131) in complex with single-chain variable 4 (scFv-4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G8R 6g8r 5ud7 experimental model PDB 5UD7 6g8r 5ud7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 39% MPD -- 0.2M ammonium acetate -- 0.1M citrate pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.92 68.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.51 α = 90 b = 180.77 β = 90 c = 125.51 γ = 90
Symmetry Space Group P 21 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 2019-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9688 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.07 83.75 99.83 0.3059 0.119 0.991 6.83 6.4 71788 69.7
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 3.07 3.18 99.9 0.558 6.6
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 6g8r 5ud7 3.07 75.99 1.34 71715 3515 99.84 0.2742 0.2735 0.2709 0.2878 0.2858 88.14
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 12.2452 f_angle_d 0.3915 f_chiral_restr 0.0375 f_plane_restr 0.0028 f_bond_d 0.0012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15649 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement PHASER phasing xia2 data processing Coot model building DIALS data reduction DIALS data scaling