3T4B | pdb_00003t4b

Crystal Structure of the HCV IRES pseudoknot domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	RNA was mixed in a 1:1 ratio with well solution (0.5-0.6 M Li2SO4, 30-37 mM MgCl2, 1-2 mM spermine, 50 mM MES, pH 6.5) with an additional 10 mM NiCl2 added to the drop before equilibration, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
5.2	76.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.39	α = 90
b = 113.39	β = 90
c = 88.22	γ = 90

Symmetry
Space Group	P 41 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	CCD	ADSC QUANTUM 315r		2011-03-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1159, 1.4855, 1.4370	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.55	100	99.5			7384	7348		-3

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	3.55	3.64	99.8		0.757	3.02	8.7	515

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	MAD	3.55	40.089	1.99	7319	7317	366	99.65	0.2227	0.2211	0.2114	0.2542	0.2435	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]
-11.0892			-11.0892		22.1785

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.423
f_angle_d	0.769
f_chiral_restr	0.054
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1796
Solvent Atoms
Heterogen Atoms	17

Software

Software
Software Name	Purpose
Blu-Ice	data collection
SOLVE	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling