9F2R | pdb_00009f2r

Influenza A/H17N10 polymerase with bound promoter and 3' end of template in active site

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	5 mg/ml polymerase with 5.1 mg/ml (19.5 microM) with 1.14 x molar excess of each RNA (v5' 1-16, v3' 1-18+3 and 15-mer capped primer), mixed in 1:1 ratio of 100 mM amino acids, 100 mM Tris/Bicine pH8.5, 8% ethylene glycol (v/v), 4% PEG 8000 (w/v) by hanging drop at room temperature

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.08	α = 90
b = 119.267	β = 90
c = 251.555	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		2019-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.959	125.799	69.7	0.159	0.166	0.997	9.7	13.3		135837

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.965	2.189	68.4		1.227	1.29	0.736	1.8	10.7

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	1.959	125.799	135837	6693	69.07	0.192	0.1892	0.1972	0.2455	0.2498	45.222

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]
-0.06			0.204		-0.144

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.967
r_dihedral_angle_6_deg	13.801
r_lrange_it	8.108
r_lrange_other	8.086
r_dihedral_angle_1_deg	6.778
r_dihedral_angle_2_deg	6.635
r_scangle_it	5.635
r_scangle_other	5.635
r_mcangle_it	5.147
r_mcangle_other	5.147
r_scbond_it	3.453
r_scbond_other	3.453
r_mcbond_it	3.27
r_mcbond_other	3.27
r_angle_refined_deg	1.407
r_angle_other_deg	0.487
r_dihedral_angle_other_2_deg	0.257
r_nbd_refined	0.217
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.153
r_nbd_other	0.152
r_symmetry_nbd_refined	0.143
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.053
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17427
Nucleic Acid Atoms	631
Solvent Atoms	1093
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling