6EUV

Structure of the midlink and cap-binding domains of influenza A polymerase PB2 subunit with a bound azaindole cap-binding inhibitor (VX-787)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EUX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	Crystals were obtained by mixing protein at 16 mg per mL mixed with 2 mM VX-787 in 0.1 M MES pH6, 0.7 M sodium formate pH 6.

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.49	α = 89.54
b = 80.32	β = 107.12
c = 92.32	γ = 99.11

Symmetry
Space Group	P 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		2017-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966	ESRF	MASSIF-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	2.7	50	94.8	0.091	0.991	5.99	1.69		38468

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	2.7	2.77	94.2		0.698	0.508	1.02	1.55

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6EUX	2.7	43.35	36631	1837	94.83	0.24469	0.2428	0.25	0.28168	0.29	RANDOM	49.627

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]
-0.24	0.95	-1.09	3.2	0.72	-2.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.89
r_dihedral_angle_3_deg	16.121
r_dihedral_angle_4_deg	15.992
r_long_range_B_refined	7.623
r_long_range_B_other	7.622
r_dihedral_angle_1_deg	6.377
r_scangle_other	5.062
r_mcangle_it	4.93
r_mcangle_other	4.93
r_scbond_it	3.105
r_scbond_other	3.105
r_mcbond_it	3.062
r_mcbond_other	3.053
r_angle_refined_deg	1.491
r_angle_other_deg	0.953
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	8713
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	178

Software

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