3AJF | pdb_00003ajf

Structural insigths into dsRNA binding and RNA silencing suppression by NS3 protein of rice hoja blanca tenuivirus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	Sulfate, MPD, cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.69	α = 90
b = 79.69	β = 90
c = 122.087	γ = 90

Symmetry
Space Group	P 41 21 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		2009-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9792	SSRF	BL17U

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	50	100	0.109		7.5	25361	25361	2	2

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	2.03	100		0.429		7.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2	34.21	25361	25361	1349	98.37	0.214	0.2144	0.21232	0.2135	0.25474	0.2564	RANDOM	22.881

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]
-0.56			-0.56		1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.321
r_dihedral_angle_4_deg	19.512
r_dihedral_angle_3_deg	14.024
r_scangle_it	4.466
r_dihedral_angle_1_deg	4.462
r_scbond_it	3.38
r_mcangle_it	1.675
r_angle_refined_deg	1.534
r_mcbond_it	1.342
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.321
r_dihedral_angle_4_deg	19.512
r_dihedral_angle_3_deg	14.024
r_scangle_it	4.466
r_dihedral_angle_1_deg	4.462
r_scbond_it	3.38
r_mcangle_it	1.675
r_angle_refined_deg	1.534
r_mcbond_it	1.342
r_nbtor_refined	0.315
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.215
r_symmetry_hbond_refined	0.214
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.1
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2998
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	40

Software

Software
Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
REFMAC	refinement
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.