1V0Z

Structure of Neuraminidase from English duck subtype N6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NNAPDB ENTRY 1NNA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120 PERCENT (W/V) PEG 3350, 150 MM NACL
Crystal Properties
Matthews coefficientSolvent content
2.4850.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.482α = 90
b = 73.755β = 90.37
c = 106.809γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH1995-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX7.2SRSPX7.2

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
11.8419.961000.077.86.712709418.1
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)
11.841.891000.163.42.1

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 1NNA1.8419.9612709466961000.1510.1490.19RANDOM15.07
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]
-1.020.042.34-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.186
r_dihedral_angle_4_deg16.132
r_dihedral_angle_3_deg12.534
r_dihedral_angle_1_deg7.18
r_scangle_it2.84
r_scbond_it1.828
r_angle_refined_deg1.428
r_mcangle_it1.038
r_mcbond_it0.656
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.186
r_dihedral_angle_4_deg16.132
r_dihedral_angle_3_deg12.534
r_dihedral_angle_1_deg7.18
r_scangle_it2.84
r_scbond_it1.828
r_angle_refined_deg1.428
r_mcangle_it1.038
r_mcbond_it0.656
r_nbtor_refined0.306
r_nbd_refined0.215
r_symmetry_vdw_refined0.188
r_symmetry_hbond_refined0.145
r_xyhbond_nbd_refined0.142
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12036
Nucleic Acid Atoms
Solvent Atoms1798
Heterogen Atoms513

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing