3G7T

Crystal structure of dengue virus type 1 envelope protein in the postfusion conformation

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OK8	PDB entry 1OK8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	289	12.5% PEG 550 MME, 0.1 M MES pH 6.5, 10 mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.65	α = 90
b = 75.65	β = 90
c = 292.802	γ = 120

Symmetry
Space Group	P 63 2 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 315	Kohzu HLD*-24 monchromator followed by vertical and horizontal focusing mirrors	2007-07-20	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315	Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator	2007-08-25	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97949	APS	24-ID-C
2	SYNCHROTRON	NSLS BEAMLINE X25	0.97949	NSLS	X25

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
1,2	3.5	50	98.7	0.223		12.1	6794	6794			73.8

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)
1,2	3.5	3.63	92		0.783	1.64	7.1	607

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1OK8	3.5	25	6786	6786	311	98.32	0.212	0.208	0.297	RANDOM	63.849

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]
-4.11	-2.06		-4.11		6.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	46.066
r_dihedral_angle_3_deg	26.037
r_dihedral_angle_4_deg	16.424
r_scangle_it	13.366
r_mcangle_it	11.621
r_dihedral_angle_1_deg	9.401
r_scbond_it	8.8
r_mcbond_it	7.201
r_angle_refined_deg	1.688
r_chiral_restr	0.114

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	46.066
r_dihedral_angle_3_deg	26.037
r_dihedral_angle_4_deg	16.424
r_scangle_it	13.366
r_mcangle_it	11.621
r_dihedral_angle_1_deg	9.401
r_scbond_it	8.8
r_mcbond_it	7.201
r_angle_refined_deg	1.688
r_chiral_restr	0.114
r_bond_refined_d	0.018
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2905
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.