5W73

Crystal structure of the influenza virus PA endonuclease in complex with inhibitor 9f (SRI-29835)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82910.1 M HEPES pH 7.8, 1.0M Ammonium Sulfate, 10 mM MnCl2, 10 mM MgCl2, 1% PVP K15
Crystal Properties
Matthews coefficientSolvent content
2.9458.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.843α = 90
b = 89.843β = 90
c = 135.002γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2017-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.000APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.25099.90.0560.0610.02311.97.21436554.21
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2898.90.9381.0190.3880.7536.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.20240.2361.341435768199.790.21870.21710.248382.2009
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.637
f_angle_d0.82
f_chiral_restr0.054
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1429
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms48

Software

Software
Software NamePurpose
PHENIXrefinement
SERGUIdata collection
HKL-2000data processing
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling