6DCY

The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 5-hydroxy-2-methyl-4-oxo-4H-pyran-3-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, 25-40% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.2144.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.54α = 90
b = 75.54β = 90
c = 120.36γ = 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)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
12.0837.771000.08319.116.912849
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)
12.082.141000.7863.418.1

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 4AWM2.0837.771204561198.740.227140.224680.2714RANDOM44.595
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]
-0.43-0.22-0.431.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.458
r_dihedral_angle_4_deg23.931
r_dihedral_angle_3_deg18.928
r_long_range_B_refined8.56
r_long_range_B_other8.557
r_scangle_other6.799
r_dihedral_angle_1_deg6.144
r_mcangle_it4.936
r_mcangle_other4.934
r_scbond_it4.726
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.458
r_dihedral_angle_4_deg23.931
r_dihedral_angle_3_deg18.928
r_long_range_B_refined8.56
r_long_range_B_other8.557
r_scangle_other6.799
r_dihedral_angle_1_deg6.144
r_mcangle_it4.936
r_mcangle_other4.934
r_scbond_it4.726
r_scbond_other4.724
r_mcbond_it3.491
r_mcbond_other3.485
r_angle_refined_deg1.425
r_angle_other_deg0.961
r_chiral_restr0.07
r_bond_refined_d0.01
r_gen_planes_refined0.007
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 Atoms1468
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing