4JK0 | pdb_00004jk0

Crystal structure of T89Q-mutant of RNA silencing suppressor p19 with 2nt-5'-overhanging double-helical RNA 21mer pUUUG(CUG)5CU

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R9F	PDB ENTRY 1R9F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	291	1.6 M ammonium sulfate, 0.1 M citric acid, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.391	α = 90
b = 90.391	β = 90
c = 148.909	γ = 120

Symmetry
Space Group	H 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	CCD	ADSC QUANTUM 315r			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9724	ESRF	ID23-1

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	2.3	30	98.6	0.118	9.1	2.7		10511

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	2.3	2.38	98.5		0.63		2.7	1021

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	PDB ENTRY 1R9F	2.3	15	10506	505	98.45	0.1867	0.1836	0.19	0.2455	0.25	RANDOM	43.1562

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]
0.9	0.9		0.9		-2.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.652
r_dihedral_angle_4_deg	16.81
r_dihedral_angle_3_deg	15.668
r_dihedral_angle_1_deg	5.645
r_mcangle_it	3.16
r_mcbond_it	2.042
r_mcbond_other	2.041
r_angle_refined_deg	1.55
r_angle_other_deg	0.99
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.652
r_dihedral_angle_4_deg	16.81
r_dihedral_angle_3_deg	15.668
r_dihedral_angle_1_deg	5.645
r_mcangle_it	3.16
r_mcbond_it	2.042
r_mcbond_other	2.041
r_angle_refined_deg	1.55
r_angle_other_deg	0.99
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	976
Nucleic Acid Atoms	439
Solvent Atoms	187
Heterogen Atoms	10

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
REFMAC	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.