6E6V

The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 3-hydroxy-6-methyl-4-oxo-1,4-dihydropyridine-2-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 DROP7.830628% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.244.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.51α = 90
b = 75.51β = 90
c = 120.16γ = 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 5.0.10.97ALS5.0.1

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
12.2544.241000.0480.050.01538.919.110206
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)
12.252.321000.5320.560.1756.419

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 4AWM2.2544.24965152099.960.21390.211580.25707RANDOM48.644
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]
-0.19-0.09-0.190.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.414
r_dihedral_angle_4_deg19.346
r_dihedral_angle_3_deg17.559
r_long_range_B_refined7.703
r_long_range_B_other7.683
r_scangle_other6.294
r_dihedral_angle_1_deg5.95
r_mcangle_it5.083
r_mcangle_other5.081
r_scbond_it4.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.414
r_dihedral_angle_4_deg19.346
r_dihedral_angle_3_deg17.559
r_long_range_B_refined7.703
r_long_range_B_other7.683
r_scangle_other6.294
r_dihedral_angle_1_deg5.95
r_mcangle_it5.083
r_mcangle_other5.081
r_scbond_it4.225
r_scbond_other4.222
r_mcbond_it3.652
r_mcbond_other3.652
r_angle_refined_deg1.316
r_angle_other_deg0.927
r_chiral_restr0.062
r_bond_refined_d0.01
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 Atoms1487
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing