3VBO | pdb_00003vbo

Crystal structure of formaldehyde treated empty human Enterovirus 71 particle (cryo at 100K)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BEV	STARTING MODEL 1BEV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	200 mM Ammonium phosphate monobasic, 24% (v/v) Isopropanol and 100 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 353.1	α = 90
b = 353.1	β = 90
c = 353.1	γ = 90

Symmetry
Space Group	P 42 3 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	PIXEL	DECTRIS PILATUS 6M		2011-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9750	Diamond	I24

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	2.88	50	99.6	0.382	6	23.5		167672		-1.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.88	2.98	97.7		1.2	20.1	16211

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	STARTING MODEL 1BEV	2.88	49.94	167005	1680	99.4	0.227	0.227	0.22	0.236	0.22	RANDOM	64.6

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]

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.3
c_scangle_it	16.1
c_scbond_it	12.89
c_mcangle_it	10.89
c_mcbond_it	7.49
c_angle_deg	1.6
c_improper_angle_d	1.02
c_bond_d	0.011
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5397
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	1

Software

Software
Software Name	Purpose
GDA	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling