2Z65 | pdb_00002z65

Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z62	PDB ENTRY 2Z62, 2Z64
experimental model	PDB	2Z64	PDB ENTRY 2Z62, 2Z64

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.5	296	0.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.192	α = 90
b = 80.987	β = 93.01
c = 107.762	γ = 90

Symmetry
Space Group	P 1 21 1

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 315	mirrors	2007-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

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	2.7	50	90.4	0.089		3	30860	27898

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2Z62, 2Z64	2.7	20	27898	1462	92.35	0.2403	0.23763	0.2308	0.28874	0.2817	RANDOM	50.542

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]
2.91		-1.93	-2.26		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.442
r_dihedral_angle_3_deg	18.508
r_dihedral_angle_4_deg	17.737
r_scangle_it	9.905
r_scbond_it	6.769
r_dihedral_angle_1_deg	6.584
r_mcangle_it	4.228
r_mcbond_it	2.658
r_angle_refined_deg	1.393
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.26
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.172
r_symmetry_hbond_refined	0.16
r_chiral_restr	0.087
r_bond_refined_d	0.01
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6646
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	287

Software

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