6IF5

Crystal structure of monkey TLR7 in complex with 2',3'-cGMP (Guanosine 2',3'-cyclic phosphate)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG 4000, ammonium sulfate, sodium citrate pH 5.0, Tris-HCl pH 7.5 and NaCl
Crystal Properties
Matthews coefficientSolvent content
2.7455.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.285α = 90
b = 139.039β = 90
c = 150.3γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1.0000SPring-8BL32XU

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
125010017.86.8133746
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.03

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT247.18133746684399.970.179910.177810.22162RANDOM41.313
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]
-0.330.190.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.247
r_dihedral_angle_4_deg22.506
r_dihedral_angle_3_deg15.566
r_long_range_B_refined8.491
r_long_range_B_other8.426
r_dihedral_angle_1_deg7.366
r_scangle_other6.771
r_scbond_it4.845
r_scbond_other4.666
r_mcangle_other4.453
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.247
r_dihedral_angle_4_deg22.506
r_dihedral_angle_3_deg15.566
r_long_range_B_refined8.491
r_long_range_B_other8.426
r_dihedral_angle_1_deg7.366
r_scangle_other6.771
r_scbond_it4.845
r_scbond_other4.666
r_mcangle_other4.453
r_mcangle_it4.452
r_mcbond_it3.45
r_mcbond_other3.444
r_angle_refined_deg1.621
r_angle_other_deg0.932
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms12533
Nucleic Acid Atoms
Solvent Atoms824
Heterogen Atoms403

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing