Experiment: 1DDL

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Turnip yellow mosaic virus

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP	4.8	295	2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, POTASSIUM PHOSPHATE BUFFER, pH 4.8, VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.78	67.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 348.546	α = 90
b = 348.546	β = 90
c = 348.546	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	295	IMAGE PLATE	MARRESEARCH		1996-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1		SSRL	BL7-1

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	2.7	40	68.7	0.107	7.3	3.2	178705	178705			23.7

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)
	2.7	2.8	82.7		0.453		2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	THROUGHOUT	TURNIP YELLOW MOSAIC VIRUS	2.7	40	1.5	3	178705	134454	13357	68.7	0.206	0.152	0.151	0.17	0.159	0.17	RANDOM	33.3

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
x_dihedral_angle_d_na	39.3
x_scangle_it	23.41
x_dihedral_angle_d	20.3
x_dihedral_angle_d_prot	20.3
x_scbond_it	13.71
x_mcangle_it	5.86
x_mcbond_it	3.61
x_improper_angle_d_na	2.93
x_angle_deg_na	2.38
x_angle_deg	1.9

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4203
Nucleic Acid Atoms	182
Solvent Atoms	285
Heterogen Atoms

Software

Software
Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

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.