6Y6C

TREM2 extracellular domain (19-174) in complex with single-chain variable fragment (scFv-4)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293.150.2M potassium chloride, 35% pentaerythritol propoxylate 5/4, 0.1M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
4.773.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.661α = 90
b = 111.661β = 90
c = 232.196γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.26100.6399.80.21290.2180.9999.9621.46949639.46
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.262.3410.694

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5UD7 6G8R2.26100.631.3469496345299.650.19240.19110.21642.78
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.1786
f_angle_d0.4968
f_chiral_restr0.0407
f_plane_restr0.0032
f_bond_d0.0019
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5382
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms14

Software

Software
Software NamePurpose
PHASERphasing
PHENIXrefinement
PHENIXdata processing
Cootmodel building
xia2data processing
xia2data reduction
DIALSdata scaling