2I69 | pdb_00002i69

Crystal structure of the West Nile virus envelope glycoprotein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZTX	PDB ENTRIES 1ZTX, 1UZG AND 1OAN
experimental model	PDB	1UZG	PDB ENTRIES 1ZTX, 1UZG AND 1OAN
experimental model	PDB	1OAN	PDB ENTRIES 1ZTX, 1UZG AND 1OAN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	293	15% (v/v) isopropanol, 0.1 M HEPES pH 7.5, and 0.2 M Na citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
3.99	69.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.262	α = 90
b = 93.262	β = 90
c = 159.319	γ = 90

Symmetry
Space Group	P 41 21 2

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 4	DOUBLY FOCUSING TOROIDAL MIRROR	2006-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C		NSLS	X26C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.11	25	94.7	0.111	14.62	8.1		13289			86.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.11	3.23	96.4		0.721	2.48	8.1

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1ZTX, 1UZG AND 1OAN	3.11	24.06	13883	11858	618	94.8	0.209	0.206	0.2	0.268	0.26	RANDOM	117.633

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]
0.79			0.79		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.385
r_dihedral_angle_3_deg	23.105
r_dihedral_angle_4_deg	20.159
r_dihedral_angle_1_deg	7.35
r_scangle_it	5.286
r_mcangle_it	5.142
r_scbond_it	3.378
r_mcbond_it	3.169
r_angle_refined_deg	1.676
r_nbtor_refined	0.321
r_symmetry_vdw_refined	0.253
r_nbd_refined	0.248
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.107
r_symmetry_hbond_refined	0.049
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
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	3043
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	38

Software

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