6E6X

The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 1-(4-(1H-tetrazol-5-yl)phenyl)-5-hydroxy-2-methylpyridin-4(1H)-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AWMPDB entry 4AWM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.830630% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.244.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.34α = 90
b = 75.34β = 90
c = 120.61γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.00ALS5.0.2

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
12.544.291000.0950.10.03219.217.57520
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.61000.4630.4870.155.719.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 4AWM2.544.29695050799.490.210450.20650.26493RANDOM48.708
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]
-0.29-0.14-0.290.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.358
r_dihedral_angle_4_deg22.152
r_dihedral_angle_3_deg16.371
r_long_range_B_refined9.211
r_long_range_B_other9.208
r_scangle_other7.25
r_dihedral_angle_1_deg6.113
r_mcangle_it4.928
r_mcangle_other4.925
r_scbond_it4.616
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.358
r_dihedral_angle_4_deg22.152
r_dihedral_angle_3_deg16.371
r_long_range_B_refined9.211
r_long_range_B_other9.208
r_scangle_other7.25
r_dihedral_angle_1_deg6.113
r_mcangle_it4.928
r_mcangle_other4.925
r_scbond_it4.616
r_scbond_other4.613
r_mcbond_other3.316
r_mcbond_it3.314
r_angle_refined_deg1.589
r_angle_other_deg1.059
r_chiral_restr0.092
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1459
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing