6VMZ

Crystal Structure of a H5N1 influenza virus hemagglutinin with CBS1117


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FKOPDB entry 2FKO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298100 mM Tris, pH 8.5, 20% PEG6000, 10% glycerol
Crystal Properties
Matthews coefficientSolvent content
3.2456.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.71α = 90
b = 126.083β = 90
c = 249.639γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2016-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.978720APS21-ID-G

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
12.229.4794.10.0840.0920.99812.285.49110799
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)
12.22.3291.20.6450.7140.7552.345.35

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 2FKO2.229.47104199542693.450.21020.2080.2518RANDOM49.644
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]
-0.481.37-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.367
r_dihedral_angle_4_deg16.68
r_dihedral_angle_3_deg15.821
r_dihedral_angle_1_deg7.021
r_angle_refined_deg1.506
r_angle_other_deg1.236
r_chiral_restr0.067
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.367
r_dihedral_angle_4_deg16.68
r_dihedral_angle_3_deg15.821
r_dihedral_angle_1_deg7.021
r_angle_refined_deg1.506
r_angle_other_deg1.236
r_chiral_restr0.067
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11616
Nucleic Acid Atoms
Solvent Atoms435
Heterogen Atoms172

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction