9TL1 | pdb_00009tl1

Structure of duck RIG-I (delta CARDs) bound to 31-mer RNA mismatched hairpin with 5'ppA-U blunt end mimicking the influenza B virus vRNA promoter (panhandle) and to ADP.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4A36

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		288	Na-citrate pH 5.5 PEG 3000 22 % NDSB 201 0,1M

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.883	α = 90
b = 100.026	β = 90
c = 190.128	γ = 90

Symmetry
Space Group	C 2 2 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		2014-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9791	ESRF	ID29

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	1.704	95.064	77	0.109	0.922	8.6	16.9		70381

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	1.704	1.859			1.024	0.566	1.5

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	1.704	95.064	70380	3472	76.99	0.187	0.1853	0.1929	0.2252	0.2289	32.057

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]
0.078			0.02		-0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	20.849
r_dihedral_angle_6_deg	15.409
r_dihedral_angle_3_deg	13.599
r_lrange_it	7.621
r_lrange_other	7.602
r_dihedral_angle_2_deg	7.164
r_dihedral_angle_1_deg	6.452
r_scangle_it	5.583
r_scangle_other	5.582
r_mcangle_it	4.046
r_mcangle_other	4.046
r_scbond_it	3.558
r_scbond_other	3.558
r_mcbond_it	2.615
r_mcbond_other	2.613
r_angle_refined_deg	1.593
r_angle_other_deg	0.541
r_symmetry_nbd_refined	0.309
r_dihedral_angle_other_2_deg	0.287
r_nbd_other	0.257
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.199
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.17
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.076
r_symmetry_xyhbond_nbd_other	0.016
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_metal_ion_refined	0.006
r_symmetry_metal_ion_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5435
Nucleic Acid Atoms	557
Solvent Atoms	333
Heterogen Atoms	42

Software

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