3B7E

Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HTYPDB ENTRY 2HTY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.329520% PEG3000, pH 7.30, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.6753.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.044α = 90
b = 129.247β = 90
c = 118.845γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror; single crystal Si(111) bent monochromator2007-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97945SSRLBL11-1

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
11.455097.60.0968.56.8160198155978
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)
11.451.4986.30.5275.6

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 2HTY1.4529.71148122780797.540.141140.140140.16015RANDOM9.675
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]
-0.611.1-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.515
r_dihedral_angle_4_deg12.932
r_dihedral_angle_3_deg11.564
r_dihedral_angle_1_deg7.308
r_scangle_it4.161
r_scbond_it3.049
r_mcangle_it1.873
r_angle_refined_deg1.441
r_mcbond_it1.318
r_angle_other_deg0.937
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.515
r_dihedral_angle_4_deg12.932
r_dihedral_angle_3_deg11.564
r_dihedral_angle_1_deg7.308
r_scangle_it4.161
r_scbond_it3.049
r_mcangle_it1.873
r_angle_refined_deg1.441
r_mcbond_it1.318
r_angle_other_deg0.937
r_mcbond_other0.423
r_symmetry_vdw_other0.246
r_nbd_other0.207
r_nbd_refined0.199
r_nbtor_refined0.178
r_symmetry_hbond_refined0.153
r_xyhbond_nbd_refined0.135
r_symmetry_vdw_refined0.13
r_nbtor_other0.092
r_chiral_restr0.088
r_metal_ion_refined0.069
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5928
Nucleic Acid Atoms
Solvent Atoms939
Heterogen Atoms143

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection