7AS1

Influenza A PB2 (F404Y mutation) in complex with VX-787


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4P1U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5291.15Magnesium chloride, Calcium chloride, Tris (base), BICINE, PEG 500, PEG 20000
Crystal Properties
Matthews coefficientSolvent content
1.9536.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 29.5α = 71.89
b = 37.25β = 69.8
c = 38.39γ = 75.17
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2019-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.541870

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
11.534.93980.0350.0420.99818.272.5382263721.017
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)
11.51.5491.20.0930.1310.9764.051.29

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 REPLACEMENTTHROUGHOUT4P1U1.534.9321508112998.240.15160.14990.185RANDOM16.849
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]
0.18-0.620.130.53-0.19-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.461
r_dihedral_angle_4_deg16.712
r_dihedral_angle_3_deg11.359
r_dihedral_angle_1_deg7.056
r_angle_refined_deg1.877
r_angle_other_deg1.575
r_chiral_restr0.095
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.461
r_dihedral_angle_4_deg16.712
r_dihedral_angle_3_deg11.359
r_dihedral_angle_1_deg7.056
r_angle_refined_deg1.877
r_angle_other_deg1.575
r_chiral_restr0.095
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1271
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing