2Z62 | pdb_00002z62

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZIW	PDB ENTRY 1ZIW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	296	0.2M NaCl, 0.1M Bis-Tris Propane, 33% PEG 1000, pH 5.50, VAPOR DIFFUSION, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.89

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210		2006-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 4A	1.0	PAL/PLS	4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.7	50	99.1	0.06		6.6		29573

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1ZIW	1.7	20	29841	29573	1588	99.1	0.19	0.19	0.19	0.208	RANDOM	27.115

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			-0.5		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.843
r_dihedral_angle_4_deg	19.356
r_dihedral_angle_3_deg	13.485
r_dihedral_angle_1_deg	5.275
r_angle_refined_deg	1.188
r_nbtor_refined	0.317
r_symmetry_hbond_refined	0.304
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.078
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
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 Atoms	Number
Protein Atoms	2189
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	115

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling