5FML

Crystal structure of the endonuclease from the PA subunit of influenza B virus bound to the PB2 subunit NLS peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WRTPDB ENTRY 4WRT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1 M MES PH 6.5, 25% PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.754.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.38α = 90
b = 80.85β = 97.15
c = 37.91γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-1ESRFMASSIF-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
11.75098.20.0312.682.7222279
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)
11.71.76930.561.842.71

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 4WRT1.740.4221181109895.60.226770.224350.27556RANDOM32.895
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]
-0.52-0.270.480.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.444
r_dihedral_angle_3_deg15.267
r_dihedral_angle_4_deg15.068
r_dihedral_angle_1_deg6.006
r_mcangle_it3.448
r_scbond_it3.235
r_mcbond_it2.35
r_mcbond_other2.35
r_angle_refined_deg1.504
r_angle_other_deg0.969
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.444
r_dihedral_angle_3_deg15.267
r_dihedral_angle_4_deg15.068
r_dihedral_angle_1_deg6.006
r_mcangle_it3.448
r_scbond_it3.235
r_mcbond_it2.35
r_mcbond_other2.35
r_angle_refined_deg1.504
r_angle_other_deg0.969
r_chiral_restr0.094
r_bond_refined_d0.012
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1741
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing