3BEQ

Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52950.16 M calcium acetate; 0.08 M cacodylate; 14.4% PEG8000; 20% glycerol, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.8356.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.728α = 90
b = 138.472β = 90
c = 117.86γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2006-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-21.00797SSRLBL9-2

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
11.645097.30.0939.14.2116395113144
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)
11.641.6876.40.5282.8

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 2HTY1.6444.86107399565297.130.181830.180310.21045RANDOM19.142
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]
-1.412.57-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.096
r_dihedral_angle_3_deg11.974
r_dihedral_angle_4_deg10.475
r_dihedral_angle_1_deg7.042
r_scangle_it5.354
r_scbond_it3.776
r_mcangle_it2.475
r_mcbond_it1.556
r_angle_refined_deg1.436
r_symmetry_vdw_other0.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.096
r_dihedral_angle_3_deg11.974
r_dihedral_angle_4_deg10.475
r_dihedral_angle_1_deg7.042
r_scangle_it5.354
r_scbond_it3.776
r_mcangle_it2.475
r_mcbond_it1.556
r_angle_refined_deg1.436
r_symmetry_vdw_other0.212
r_nbd_other0.202
r_nbd_refined0.199
r_mcbond_other0.189
r_nbtor_refined0.18
r_symmetry_hbond_refined0.168
r_symmetry_vdw_refined0.158
r_xyhbond_nbd_refined0.142
r_chiral_restr0.102
r_nbtor_other0.093
r_metal_ion_refined0.09
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_gen_planes_other0.001
r_bond_other_d
r_angle_other_deg
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 Atoms754
Heterogen Atoms154

Software

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