9TEL | pdb_00009tel

Structure of chicken LGP2 bound to 10-mer RNA mismatched duplex that mimics the influenza B virus vRNA promoter (panhandle) and to ADP-AlF4-Mg.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JB2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	Directly after size exclusion chromatography, chLGP2 was mixed with duplex RNA in a 1:1 ratio and incubated for 30 minutes on ice. The complexes were concentrated to around 10 mg/ml and then 2 mM ADP:AlF4 and 2 mM MgCl2 were added. The complex was mixed with reservoir solution (0.1M Na citrate pH 6.1 0.46 M NH4 dihydrophosphate) in a ratio 1:2.

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.9	α = 90
b = 96.462	β = 90
c = 122.324	γ = 90

Symmetry
Space Group	P 21 21 21

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		2014-09-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97924	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.436	75.744	78.1	0.052	0.997	11.2	3.8		117940

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.436	1.557	18.2		0.719	0.673	1.6	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.436	75.744	117939	5833	78.118	0.149	0.1478	0.148	0.1785	0.1783	22.583

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]
-0.968			-0.219		1.187

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	17.823
r_dihedral_angle_6_deg	14.058
r_lrange_it	13.466
r_lrange_other	11.822
r_dihedral_angle_3_deg	11.621
r_scangle_it	6.309
r_scangle_other	6.309
r_dihedral_angle_1_deg	6.134
r_mcangle_it	5.663
r_mcangle_other	5.662
r_dihedral_angle_2_deg	4.904
r_scbond_it	3.958
r_scbond_other	3.958
r_mcbond_it	3.438
r_mcbond_other	3.437
r_rigid_bond_restr	1.809
r_angle_refined_deg	1.242
r_angle_other_deg	0.452
r_dihedral_angle_other_2_deg	0.399
r_symmetry_nbd_refined	0.317
r_nbd_refined	0.249
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.169
r_nbd_other	0.152
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.062
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5294
Nucleic Acid Atoms	420
Solvent Atoms	714
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing