9F2R

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6EVJ 

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), 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 coefficientSolvent content
2.4750.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.08α = 90
b = 119.267β = 90
c = 251.555γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.959125.79969.70.1590.1660.9979.713.3135837
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)
11.9652.18968.41.2271.290.7361.810.7

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-VALUE1.959125.799135837669369.070.1920.18920.245545.222
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]
-0.060.204-0.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.967
r_dihedral_angle_6_deg13.801
r_lrange_it8.108
r_lrange_other8.086
r_dihedral_angle_1_deg6.778
r_dihedral_angle_2_deg6.635
r_scangle_it5.635
r_scangle_other5.635
r_mcangle_it5.147
r_mcangle_other5.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.967
r_dihedral_angle_6_deg13.801
r_lrange_it8.108
r_lrange_other8.086
r_dihedral_angle_1_deg6.778
r_dihedral_angle_2_deg6.635
r_scangle_it5.635
r_scangle_other5.635
r_mcangle_it5.147
r_mcangle_other5.147
r_scbond_it3.453
r_scbond_other3.453
r_mcbond_it3.27
r_mcbond_other3.27
r_angle_refined_deg1.407
r_angle_other_deg0.487
r_dihedral_angle_other_2_deg0.257
r_nbd_refined0.217
r_symmetry_nbd_other0.19
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.16
r_symmetry_xyhbond_nbd_refined0.153
r_nbd_other0.152
r_symmetry_nbd_refined0.143
r_symmetry_nbtor_other0.078
r_chiral_restr0.069
r_symmetry_xyhbond_nbd_other0.053
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17427
Nucleic Acid Atoms631
Solvent Atoms1093
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling