8FAQ

Structure of Hemagglutinin from Influenza A/Victoria/22/2020


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WE8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5291.1550% PEG-200, 0.1M citrate pH 5.5, final pH 6.9
Crystal Properties
Matthews coefficientSolvent content
3.3963.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.705α = 90
b = 99.705β = 90
c = 395.31γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2021-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.12723APS21-ID-D

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
12.03579.25298.60.0770.0790.99921.620.448446
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.0352.071981.6420.8652.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNONE2YP42.03579.25248446240098.5560.2040.20280.229154.981
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]
-0.005-0.003-0.0050.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.247
r_dihedral_angle_3_deg15.356
r_dihedral_angle_4_deg14.224
r_lrange_it8.29
r_scangle_it6.968
r_dihedral_angle_1_deg6.933
r_scbond_it5.072
r_mcangle_it4.935
r_mcbond_it3.901
r_angle_refined_deg1.473
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.247
r_dihedral_angle_3_deg15.356
r_dihedral_angle_4_deg14.224
r_lrange_it8.29
r_scangle_it6.968
r_dihedral_angle_1_deg6.933
r_scbond_it5.072
r_mcangle_it4.935
r_mcbond_it3.901
r_angle_refined_deg1.473
r_nbtor_refined0.313
r_nbd_refined0.215
r_symmetry_nbd_refined0.187
r_symmetry_xyhbond_nbd_refined0.15
r_xyhbond_nbd_refined0.144
r_chiral_restr0.103
r_bond_refined_d0.007
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3941
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
XDSdata scaling
PHENIXphasing