8SD2

Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with small molecule fusion inhibitor compound 4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5W5S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION62771 M lithium chloride, 0.1 M MES, pH 6, 20% wt/vol PEG6000
Crystal Properties
Matthews coefficientSolvent content
3.3963.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 166.638α = 90
b = 166.638β = 90
c = 166.638γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03317APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rpim 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
12.8144.581000.120.020.9813935.21887670
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.812.8710.450.570.8

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 REPLACEMENTTHROUGHOUT2.8144.581781399799.770.219460.216710.26126RANDOM79
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.668
r_dihedral_angle_4_deg16.873
r_dihedral_angle_3_deg15.251
r_long_range_B_other14.623
r_long_range_B_refined14.621
r_scangle_other10.502
r_mcangle_it10.306
r_mcangle_other10.306
r_scbond_it7.152
r_scbond_other7.146
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.668
r_dihedral_angle_4_deg16.873
r_dihedral_angle_3_deg15.251
r_long_range_B_other14.623
r_long_range_B_refined14.621
r_scangle_other10.502
r_mcangle_it10.306
r_mcangle_other10.306
r_scbond_it7.152
r_scbond_other7.146
r_mcbond_it7.022
r_mcbond_other7.006
r_dihedral_angle_1_deg6.833
r_angle_refined_deg1.397
r_angle_other_deg1.318
r_chiral_restr0.055
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms3783
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing