2Z62

Crystal structure of the TV3 hybrid of human TLR4 and hagfish VLRB.61


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZIWPDB ENTRY 1ZIW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.52960.2M NaCl, 0.1M Bis-Tris Propane, 33% PEG 1000, pH 5.50, VAPOR DIFFUSION, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.2344.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.945α = 90
b = 54.214β = 90
c = 116.637γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4A1.0PAL/PLS4A

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
11.75099.10.066.629573

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 1ZIW1.7202984129573158899.10.190.190.208RANDOM27.115
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]
-0.21-0.50.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.843
r_dihedral_angle_4_deg19.356
r_dihedral_angle_3_deg13.485
r_dihedral_angle_1_deg5.275
r_angle_refined_deg1.188
r_nbtor_refined0.317
r_symmetry_hbond_refined0.304
r_symmetry_vdw_refined0.235
r_nbd_refined0.197
r_xyhbond_nbd_refined0.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.843
r_dihedral_angle_4_deg19.356
r_dihedral_angle_3_deg13.485
r_dihedral_angle_1_deg5.275
r_angle_refined_deg1.188
r_nbtor_refined0.317
r_symmetry_hbond_refined0.304
r_symmetry_vdw_refined0.235
r_nbd_refined0.197
r_xyhbond_nbd_refined0.108
r_chiral_restr0.078
r_bond_refined_d0.007
r_gen_planes_refined0.003
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2189
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms115

Software

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