5WYZ

Crystal structure of human TLR8 in complex with CU-CPT9b


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG 4000, calcium chloride, Tris-HCl, ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.5351.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.62α = 90
b = 98.95β = 108.39
c = 139.52γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 315r2016-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.3132.3910012.36.678179

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2.3132.3978165419799.980.211020.208340.26004RANDOM60.223
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]
-0.020.03-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.876
r_dihedral_angle_3_deg16.546
r_dihedral_angle_4_deg15.666
r_long_range_B_other10.188
r_long_range_B_refined10.186
r_scangle_other7.634
r_dihedral_angle_1_deg7.281
r_mcangle_it6.878
r_mcangle_other6.878
r_scbond_it5.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.876
r_dihedral_angle_3_deg16.546
r_dihedral_angle_4_deg15.666
r_long_range_B_other10.188
r_long_range_B_refined10.186
r_scangle_other7.634
r_dihedral_angle_1_deg7.281
r_mcangle_it6.878
r_mcangle_other6.878
r_scbond_it5.119
r_scbond_other5.118
r_mcbond_it4.848
r_mcbond_other4.844
r_angle_refined_deg1.675
r_angle_other_deg1.075
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12042
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms361

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing