9TKV | pdb_00009tkv

Structure of duck RIG-I (delta CARDS) bound to 31-mer RNA mismatched hairpin with 5'pppG-C blunt end, mimicking the influenza B virus vRNA promoter (panhandle).

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	ADA 0.1 M MgCl2 0.1M PEG 6000 12 % ZnCl2 0.1M

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.641	α = 90
b = 100.072	β = 90
c = 192.287	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		2014-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9792	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	1.488	96.144	81.3	0.098	0.999	13.8	8.7		112184

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	1.488	1.612	19.2		1.577	0.541	1.5	9.3

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	1.488	96.144	112184	5601	81.344	0.149	0.1472	0.1472	0.1914	0.1915	25.067

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]
1.323			-1.216		-0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_mcangle_it	32.867
r_mcangle_other	32.863
r_lrange_it	26.542
r_lrange_other	26.118
r_dihedral_angle_other_3_deg	26.008
r_mcbond_it	21.213
r_mcbond_other	21.212
r_dihedral_angle_6_deg	14.814
r_dihedral_angle_3_deg	11.742
r_scangle_it	10.861
r_scangle_other	10.86
r_scbond_it	6.055
r_scbond_other	6.054
r_dihedral_angle_1_deg	5.99
r_dihedral_angle_2_deg	5.715
r_rigid_bond_restr	2.615
r_angle_refined_deg	1.387
r_angle_other_deg	0.496
r_nbd_other	0.278
r_symmetry_nbd_refined	0.272
r_nbd_refined	0.231
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.165
r_dihedral_angle_other_2_deg	0.123
r_symmetry_xyhbond_nbd_refined	0.109
r_symmetry_xyhbond_nbd_other	0.083
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.068
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5411
Nucleic Acid Atoms	671
Solvent Atoms	599
Heterogen Atoms	12

Software

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