8PUP

Influenza A/California/07/2009(H1N1) endonuclease in complex with purpurogallin-like compound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7NUG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291.15MDP, PEG 1000, PEG 3350, Sodium HEPES, MOPS (acid), Magnesium chloride, Calcium chloride
Crystal Properties
Matthews coefficientSolvent content
2.3146.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.95α = 90
b = 73.95β = 90
c = 126.61γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.9350990.0980.10099999999999999119.8517.228879
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.932.052.1672.3310.29600000000000004

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT245.021368372199.450.218310.215870.26548RANDOM44.982
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]
-0.46-0.23-0.461.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.985
r_dihedral_angle_2_deg8.24
r_long_range_B_refined7.889
r_long_range_B_other7.887
r_scangle_other6.018
r_dihedral_angle_1_deg5.852
r_mcangle_it5.397
r_mcangle_other5.394
r_scbond_it4.114
r_scbond_other4.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.985
r_dihedral_angle_2_deg8.24
r_long_range_B_refined7.889
r_long_range_B_other7.887
r_scangle_other6.018
r_dihedral_angle_1_deg5.852
r_mcangle_it5.397
r_mcangle_other5.394
r_scbond_it4.114
r_scbond_other4.111
r_mcbond_it3.995
r_mcbond_other3.988
r_angle_refined_deg1.271
r_angle_other_deg0.443
r_chiral_restr0.058
r_bond_refined_d0.009
r_bond_other_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms1450
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing