3K36

Crystal Structure of B/Perth Neuraminidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7NN9PDB ENTRY 7NN9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5281.150.2M Na2SO4, 20% w/v PEG3350, 0.1M bis-Tris propane, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 281.15K
Crystal Properties
Matthews coefficientSolvent content
2.1643.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.64α = 90
b = 87.64β = 90
c = 197.19γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmBEAMLINE OPTICS2007-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.95361Australian SynchrotronMX1

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
12.291.50.12211.64.53430634306-1-120.979
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)
2.22.3277.60.4382.72.912265

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 7NN92.298.533258032580172691.320.185110.18230.23929RANDOM17.369
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]
-1.54-1.543.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.073
r_dihedral_angle_3_deg18.274
r_dihedral_angle_4_deg17.163
r_dihedral_angle_1_deg7.942
r_scangle_it2.581
r_scbond_it1.707
r_angle_refined_deg1.56
r_mcangle_it1.053
r_angle_other_deg0.921
r_mcbond_it0.584
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.073
r_dihedral_angle_3_deg18.274
r_dihedral_angle_4_deg17.163
r_dihedral_angle_1_deg7.942
r_scangle_it2.581
r_scbond_it1.707
r_angle_refined_deg1.56
r_mcangle_it1.053
r_angle_other_deg0.921
r_mcbond_it0.584
r_mcbond_other0.137
r_chiral_restr0.091
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6012
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms188

Software

Software
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing