3GVJ

Crystal structure of an endo-neuraminidaseNF mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.229320% (w/v) PEG 8000, 0.1M Tris/HCl, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2361.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.09α = 90
b = 119.09β = 90
c = 175.98γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
11.42089.90.09164778-3
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)
11.41.546.20.3594

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.481214703677391000.195060.193950.21636RANDOM16.438
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]
0.240.120.24-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.346
r_dihedral_angle_4_deg13.912
r_dihedral_angle_3_deg11.887
r_dihedral_angle_1_deg7.095
r_scangle_it2.228
r_scbond_it1.505
r_angle_refined_deg1.471
r_mcangle_it0.88
r_mcbond_it0.515
r_chiral_restr0.131
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.346
r_dihedral_angle_4_deg13.912
r_dihedral_angle_3_deg11.887
r_dihedral_angle_1_deg7.095
r_scangle_it2.228
r_scbond_it1.505
r_angle_refined_deg1.471
r_mcangle_it0.88
r_mcbond_it0.515
r_chiral_restr0.131
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5253
Nucleic Acid Atoms
Solvent Atoms850
Heterogen Atoms182

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction