6E0Q

The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 4,6-dihydroxy-2-methyl-5-oxocyclohepta-1,3,6-triene-1-carboxylic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.53060.5 mM inhibitor, 30-32% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.3146.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.09α = 90
b = 75.09β = 90
c = 119.67γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97741ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.3544.031000.0740.335.18874
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.431000.5178.636.8

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 4AWM2.3544.03796288099.980.205840.200150.25788RANDOM44.568
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]
-0.61-0.3-0.611.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.836
r_dihedral_angle_4_deg23.199
r_dihedral_angle_3_deg18.905
r_long_range_B_refined7.219
r_long_range_B_other7.217
r_dihedral_angle_1_deg6.18
r_scangle_other5.785
r_mcangle_it4.59
r_mcangle_other4.588
r_scbond_it3.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.836
r_dihedral_angle_4_deg23.199
r_dihedral_angle_3_deg18.905
r_long_range_B_refined7.219
r_long_range_B_other7.217
r_dihedral_angle_1_deg6.18
r_scangle_other5.785
r_mcangle_it4.59
r_mcangle_other4.588
r_scbond_it3.84
r_scbond_other3.838
r_mcbond_it3.242
r_mcbond_other3.241
r_angle_refined_deg1.4
r_angle_other_deg0.961
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms1479
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing