5C0W

Structure of a 12-subunit nuclear exosome complex bound to single-stranded RNA substrates

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IFD	4IFD, 4WFC, 4WFD, 4OO1, 2VNU, 2HBJ, 4WP8
experimental model	PDB	4WFC	4IFD, 4WFC, 4WFD, 4OO1, 2VNU, 2HBJ, 4WP8
experimental model	PDB	4WFD	4IFD, 4WFC, 4WFD, 4OO1, 2VNU, 2HBJ, 4WP8
experimental model	PDB	4OO1	4IFD, 4WFC, 4WFD, 4OO1, 2VNU, 2HBJ, 4WP8
experimental model	PDB	2VNU	4IFD, 4WFC, 4WFD, 4OO1, 2VNU, 2HBJ, 4WP8
experimental model	PDB	2HBJ	4IFD, 4WFC, 4WFD, 4OO1, 2VNU, 2HBJ, 4WP8
experimental model	PDB	4WP8	4IFD, 4WFC, 4WFD, 4OO1, 2VNU, 2HBJ, 4WP8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	292	4.1-4.4%(w/v) PEG 8000, 0.1M MES pH 5.5, 0.2M KCl, 0.01M MgCl2, 283K and 292K

Crystal Properties
Matthews coefficient	Solvent content
4.96	75.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 195.38	α = 90
b = 195.38	β = 90
c = 463.65	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2014-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.2398	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	4.6	59.09	69.5	0.114	0.126	6	3.435		40273		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	4.6	4.8	24.3		0.708	1.002	0.45	1.04

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4IFD, 4WFC, 4WFD, 4OO1, 2VNU, 2HBJ, 4WP8	4.6	59.09	1.33	40199	2306	69.5	0.2773	0.2713	0.2838	Random selection	341.334

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	11.75
f_angle_d	0.99
f_chiral_restr	0.053
f_bond_d	0.013
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	30801
Nucleic Acid Atoms	352
Solvent Atoms
Heterogen Atoms	10

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building
PDB_EXTRACT	data extraction

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 R01GM133198.