7JJU | pdb_00007jju

Crystal structure of en exoribonuclease-resistant RNA (xrRNA) from Potato leafroll virus (PLRV)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1 microL RNA solution (5 mg/mL RNA in 30 mM HEPES pH 7.5, 20 mM MgCl2, 100 mM KCl) + 1 microL crystallization solution (10% 2-methyl-2,4-pentanediol, 40 mM Sodium Cacodylate (pH 6.0), 12 mM Spermine, 150 mM KCl, 100 mM Guanidinium HCl) over a reservoir of 500 microL of 30% 2-methyl-2,4-pentanediol and 100mM Guanidinium HCl.

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.19	α = 90
b = 72.19	β = 90
c = 137.14	γ = 90

Symmetry
Space Group	P 43 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	CMOS	RDI CMOS_8M		2019-09-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	0.9234	ALS	4.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.604	49.72	99.64	0.09956	0.1008	0.01561	1	30.86	41.3		11689			63.33

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.604	2.697	99.56		1.663	1.685	0.914	2.53	38

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.604	49.72	1.35	11669	1097	99.66	0.2261	0.2246	0.23	0.2534	0.26	62.95

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	15.5962
f_angle_d	0.4406
f_chiral_restr	0.0202
f_plane_restr	0.0018
f_bond_d	0.0012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	2162
Solvent Atoms
Heterogen Atoms	178

Software

Software
Software Name	Purpose
XDS	data processing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	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.