2PNZ

Crystal structure of the P. abyssi exosome RNase PH ring complexed with UDP and GMP

X-RAY DIFFRACTION

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
2.78	55.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.81	α = 90
b = 93.81	β = 90
c = 126.26	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	2006-04-01	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	2.14	43.98	99.3	0.172	11.3	14.8	36300	36060	1	1	28

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)
	2.14	2.26	96		0.639	3.3	11.8	5542

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2BA0	2.14	19.87	1	1	34174	33921	1783	99.26	0.19088	0.19088	0.18752	0.25481	RANDOM	32.856

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]
-0.02	-0.01		-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.196
r_dihedral_angle_3_deg	20.369
r_dihedral_angle_4_deg	14.232
r_dihedral_angle_1_deg	9.836
r_scangle_it	4.074
r_scbond_it	2.787
r_angle_refined_deg	2.312
r_mcangle_it	1.593
r_mcbond_it	1.037
r_nbtor_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.196
r_dihedral_angle_3_deg	20.369
r_dihedral_angle_4_deg	14.232
r_dihedral_angle_1_deg	9.836
r_scangle_it	4.074
r_scbond_it	2.787
r_angle_refined_deg	2.312
r_mcangle_it	1.593
r_mcbond_it	1.037
r_nbtor_refined	0.323
r_symmetry_vdw_refined	0.252
r_nbd_refined	0.243
r_xyhbond_nbd_refined	0.195
r_symmetry_hbond_refined	0.174
r_chiral_restr	0.164
r_bond_refined_d	0.023
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3913
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	49

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 National Science Foundation (DBI-1832184), 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.