3NYB | pdb_00003nyb

Structure and function of the polymerase core of TRAMP, a RNA surveillance complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	277	100 mM sodium citrate at pH 5.8, 200 mM sodium acetate, 11% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.72	α = 90
b = 92.72	β = 90
c = 103.63	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	110	CCD	ADSC QUANTUM 315		2009-04-19	M	SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.28215	APS	24-ID-C

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	2.6	25	100	0.077		10.6	16163	16163		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.6	2.69	100		0.082	0.86	2.3

Refinement

Statistics
Diffraction ID	Structure Solution 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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	2.7007	24.656	0.14	14108	979	96.79	0.1982	0.1935	0.191	0.2581	0.2528	random

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]
-1.0538			-1.0538		2.1076

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.127
f_angle_d	1.034
f_chiral_restr	0.07
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3079
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
SHARP	phasing
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling