4WIZ | pdb_00004wiz

Crystal structure of Grouper nervous necrosis virus-like particle at 3.6A

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	291	0.2 M Sodium formate, 20% (w/v) PEG 3350, pH7.2

Crystal Properties
Matthews coefficient	Solvent content
3.67	66.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 477.355	α = 90
b = 422.735	β = 134.03
c = 337.893	γ = 90

Symmetry
Space Group	C 1 2 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	RAYONIX MX225HE		2012-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.90	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.6	266	98.9	7.2	3.9		549703

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	AB INITIO PHASING	THROUGHOUT	3.6	263.91	549703	27556	99.25	0.2567	0.2546	0.26	0.2968	0.29	RANDOM	103.7458

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]
-0.09			-0.02		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.79
r_mcangle_it	22.371
r_dihedral_angle_3_deg	20.727
r_dihedral_angle_4_deg	17.138
r_mcbond_it	14.148
r_mcbond_other	14.148
r_dihedral_angle_1_deg	7.384
r_angle_refined_deg	1.767
r_angle_other_deg	1.062
r_chiral_restr	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.79
r_mcangle_it	22.371
r_dihedral_angle_3_deg	20.727
r_dihedral_angle_4_deg	17.138
r_mcbond_it	14.148
r_mcbond_other	14.148
r_dihedral_angle_1_deg	7.384
r_angle_refined_deg	1.767
r_angle_other_deg	1.062
r_chiral_restr	0.1
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	203160
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	90

Software

Software
Software Name	Purpose
HKL-2000	data processing
HKL-2000	data scaling
REFMAC	refinement

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.