2J67

The TIR domain of human Toll-Like Receptor 10 (TLR10)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FYVPDB ENTRY 1FYV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2 M NASCN, 11% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.8957.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.2α = 90
b = 43.3β = 101
c = 71.3γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.22397.60.0613.83.819993
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3920.43.53.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 1FYV2.223.4318992100097.80.2160.2140.266RANDOM28.04
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]
-2.02-0.931.530.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.406
r_dihedral_angle_4_deg20.217
r_dihedral_angle_3_deg15.871
r_dihedral_angle_1_deg6.933
r_scangle_it2.532
r_scbond_it2.187
r_mcangle_it1.714
r_angle_refined_deg1.524
r_mcbond_it1.356
r_angle_other_deg0.954
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.406
r_dihedral_angle_4_deg20.217
r_dihedral_angle_3_deg15.871
r_dihedral_angle_1_deg6.933
r_scangle_it2.532
r_scbond_it2.187
r_mcangle_it1.714
r_angle_refined_deg1.524
r_mcbond_it1.356
r_angle_other_deg0.954
r_nbd_refined0.226
r_nbtor_refined0.198
r_xyhbond_nbd_refined0.192
r_symmetry_vdw_other0.19
r_nbd_other0.188
r_symmetry_hbond_refined0.171
r_symmetry_vdw_refined0.144
r_chiral_restr0.097
r_nbtor_other0.086
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2345
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing