2PO1 | pdb_00002po1

Crystal structure of the P. abyssi exosome RNase PH ring complexed with a single stranded 10-mer poly(A) RNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PNZ	PDB ENTRY 2PNZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	0.1 M Bis-Tris, 45% MPD and 0.1 M LiCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.555	α = 90
b = 93.555	β = 90
c = 125.951	γ = 120

Symmetry
Space Group	P 3 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	CCD	MAR CCD 165 mm	mirrors	2006-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.427	LNLS	D03B-MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.94	46.78	98.2	0.109	14.9	11	47831	46981	1	1	23.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.94	2.06	90.1		0.627	3.5	9.2	6859

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	PDB ENTRY 2PNZ	1.94	20	1	1	45299	44547	2374	98.34	0.19016	0.19016	0.18738	0.19	0.24243	0.24	RANDOM	29.413

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]
0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.956
r_dihedral_angle_3_deg	17.827
r_dihedral_angle_4_deg	17.121
r_dihedral_angle_1_deg	6.547
r_scangle_it	3.938
r_scbond_it	2.621
r_angle_refined_deg	2.065
r_mcangle_it	1.559
r_mcbond_it	1.101
r_nbtor_refined	0.328

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.956
r_dihedral_angle_3_deg	17.827
r_dihedral_angle_4_deg	17.121
r_dihedral_angle_1_deg	6.547
r_scangle_it	3.938
r_scbond_it	2.621
r_angle_refined_deg	2.065
r_mcangle_it	1.559
r_mcbond_it	1.101
r_nbtor_refined	0.328
r_symmetry_vdw_refined	0.244
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.195
r_symmetry_hbond_refined	0.191
r_chiral_restr	0.132
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3915
Nucleic Acid Atoms	154
Solvent Atoms	348
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
XDS	data reduction
XDS	data scaling
MOLREP	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.