9F37

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

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9F2R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2935 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 coefficientSolvent content
2.4650.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.937α = 90
b = 119.005β = 90
c = 251.381γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-01-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9795DiamondI03

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.90586.671.50.0840.0910.99913.36.9151625
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)RedundancyNumber Unique Reflections (All)
11.912.110.9551.040.7081.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.90586.566151625759071.2240.1910.18910.231549.685
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]
-0.1650.223-0.058
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.745
r_dihedral_angle_6_deg14.196
r_lrange_other8.171
r_lrange_it8.169
r_dihedral_angle_2_deg7.499
r_dihedral_angle_1_deg6.876
r_scangle_it6.093
r_scangle_other6.093
r_mcangle_it5.509
r_mcangle_other5.508
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.745
r_dihedral_angle_6_deg14.196
r_lrange_other8.171
r_lrange_it8.169
r_dihedral_angle_2_deg7.499
r_dihedral_angle_1_deg6.876
r_scangle_it6.093
r_scangle_other6.093
r_mcangle_it5.509
r_mcangle_other5.508
r_scbond_it3.876
r_scbond_other3.876
r_mcbond_it3.623
r_mcbond_other3.623
r_angle_refined_deg1.458
r_angle_other_deg0.495
r_symmetry_xyhbond_nbd_refined0.245
r_nbd_refined0.219
r_dihedral_angle_other_2_deg0.189
r_symmetry_nbd_other0.188
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.164
r_nbd_other0.151
r_symmetry_nbd_refined0.133
r_symmetry_nbtor_other0.078
r_chiral_restr0.07
r_symmetry_xyhbond_nbd_other0.02
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17411
Nucleic Acid Atoms639
Solvent Atoms700
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling