Experiment: 4LLF

Crystal structure of Cucumber Necrosis Virus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2TBV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	295	Virus concentration was adjusted to 10 mg/ml in 20 mM sodium acetate buffer at pH 5.0. The reservoir contained 0.16 M PIPES buffer and 3.2 M sodium formate, pH 6.0. Drop composed of 10 microliters reservoir and virus solutions., VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.84	68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 384	α = 90
b = 384	β = 90
c = 384	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	CCD	BRUKER SMART 6000		2013-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	1.5418

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	2.889	75.309	64			140952	134159

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2TBV	2.8891	75.309	140952	134159	6793	64.36	0.2142	0.2142	0.2127	0.2121	0.2418	0.2385	RANDOM

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
f_dihedral_angle_d	16.256
f_angle_d	1.491
f_chiral_restr	0.1
f_bond_d	0.011
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	34345
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	20

Software

Software
Software Name	Purpose
PROTEUM PLUS	data collection
PHENIX	model building
PHENIX	refinement
SAINT	data reduction
SHELX	data scaling
PHENIX	phasing