6QCW

Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.4	277	Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 14-mer capped RNA. The mother liquor contained 200 mM di-ammonium phosphate and 100 mM sodium acetate between pH 4.0 and 4.4.

Crystal Properties
Matthews coefficient	Solvent content
5.33	76.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 200.354	α = 90
b = 200.354	β = 90
c = 256.466	γ = 120

Symmetry
Space Group	P 32 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	100	PIXEL	DECTRIS PILATUS 6M-F		2018-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.977	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	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	2.88	50	60.7	0.177	0.185	0.995	8.2	8.2		81417

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.88	3.12	60.9		1.42	1.5	0.677	1.8	10

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5MSG	2.88	50	77475	3942	60.68	0.21548	0.21453	0.23391	RANDOM	105.835

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]
0.07	0.03		0.07		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.094
r_dihedral_angle_3_deg	15.358
r_dihedral_angle_4_deg	13.572
r_dihedral_angle_1_deg	4.969
r_long_range_B_refined	2.138
r_long_range_B_other	2.138
r_mcangle_it	0.739
r_mcangle_other	0.739
r_angle_refined_deg	0.731
r_angle_other_deg	0.705
r_scangle_other	0.593
r_mcbond_it	0.4
r_mcbond_other	0.4
r_scbond_it	0.314
r_scbond_other	0.314
r_chiral_restr	0.034
r_bond_refined_d	0.003
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17461
Nucleic Acid Atoms	1064
Solvent Atoms
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoPROC	data scaling
PHASER	phasing