2Z63

Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z62PDB ENTRY 2Z62

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52770.2M Sodium Citrate, 0.1M Bis-Tris Propane, 27% PEG 1000, pH 6.50, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.2161.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.136α = 90
b = 88.136β = 90
c = 92.205γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1250970.083.148960

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 2Z622205047448960262295.80.2510.249610.29809RANDOM32.303
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]
-0.49-0.24-0.490.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.341
r_dihedral_angle_3_deg16.458
r_dihedral_angle_4_deg13.751
r_scangle_it5.344
r_dihedral_angle_1_deg4.994
r_scbond_it3.818
r_mcangle_it2.161
r_mcbond_it1.535
r_angle_refined_deg1.38
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.341
r_dihedral_angle_3_deg16.458
r_dihedral_angle_4_deg13.751
r_scangle_it5.344
r_dihedral_angle_1_deg4.994
r_scbond_it3.818
r_mcangle_it2.161
r_mcbond_it1.535
r_angle_refined_deg1.38
r_nbtor_refined0.319
r_symmetry_hbond_refined0.233
r_nbd_refined0.226
r_symmetry_vdw_refined0.211
r_xyhbond_nbd_refined0.156
r_chiral_restr0.092
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4536
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms66

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling