6YMQ

TREM2 extracellular domain (19-131) in complex with single-chain variable 4 (scFv-4)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1539% MPD -- 0.2M ammonium acetate -- 0.1M citrate pH 5.5
Crystal Properties
Matthews coefficientSolvent content
3.9268.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.51α = 90
b = 180.77β = 90
c = 125.51γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002019-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9688DiamondI24

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.0783.7599.830.30590.1190.9916.836.47178869.7
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)
13.073.1899.90.5586.6

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-VALUE6g8r 5ud73.0775.991.3471715351599.840.27420.27350.287888.14
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.2452
f_angle_d0.3915
f_chiral_restr0.0375
f_plane_restr0.0028
f_bond_d0.0012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15649
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms68

Software

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