9F37 | pdb_00009f37

Replication-like initiation state of influenza polymerase with GTP and CTP at respectively the -1 and +1 positions (strain A/little yellow-shouldered bat/Guatemala/060/2010/H17N10)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9F2R

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, see Figure 1a) 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. Soaking was performed with 5 mM GTP, 5 mM CTP and 5 mM MgCl2 for 5h.

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.937	α = 90
b = 119.005	β = 90
c = 251.381	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		2020-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9795	Diamond	I03

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	1.905	86.6	71.5	0.084	0.091	0.999	13.3	6.9		151625

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	1.91	2.11			0.955	1.04	0.708	1.8

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	1.905	86.566	151625	7590	71.224	0.191	0.1891	0.1968	0.2315	0.2366	49.685

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]
-0.165			0.223		-0.058

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.745
r_dihedral_angle_6_deg	14.196
r_lrange_other	8.171
r_lrange_it	8.169
r_dihedral_angle_2_deg	7.499
r_dihedral_angle_1_deg	6.876
r_scangle_it	6.093
r_scangle_other	6.093
r_mcangle_it	5.509
r_mcangle_other	5.508
r_scbond_it	3.876
r_scbond_other	3.876
r_mcbond_it	3.623
r_mcbond_other	3.623
r_angle_refined_deg	1.458
r_angle_other_deg	0.495
r_symmetry_xyhbond_nbd_refined	0.245
r_nbd_refined	0.219
r_dihedral_angle_other_2_deg	0.189
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.164
r_nbd_other	0.151
r_symmetry_nbd_refined	0.133
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.02
r_gen_planes_refined	0.006
r_bond_refined_d	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	17411
Nucleic Acid Atoms	639
Solvent Atoms	700
Heterogen Atoms	126

Software

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