1W21

Structure of Neuraminidase from English duck subtype N6 complexed with 30 mM sialic acid (NANA, Neu5Ac), crystal soaked for 43 hours at 291 K.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V0ZPDB ENTRY 1V0Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
172930.15 M NACL, 20% PEG 3350 AT 293 K, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
2.4950.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.478α = 90
b = 73.995β = 90.5
c = 106.465γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateCONFOCAL OSMIC BLUE2004-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200H

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
12.0830.4398.20.097.92.29886118.85
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)
12.082.1992.30.272.72.1

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 1V0Z2.0830.43933584913980.1530.150.195RANDOM19.39
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]
-1.59-0.432.89-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.92
r_scangle_it4.289
r_scbond_it2.998
r_angle_refined_deg2.042
r_mcangle_it1.752
r_mcbond_it1.088
r_nbd_refined0.355
r_symmetry_vdw_refined0.276
r_chiral_restr0.199
r_xyhbond_nbd_refined0.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.92
r_scangle_it4.289
r_scbond_it2.998
r_angle_refined_deg2.042
r_mcangle_it1.752
r_mcbond_it1.088
r_nbd_refined0.355
r_symmetry_vdw_refined0.276
r_chiral_restr0.199
r_xyhbond_nbd_refined0.147
r_symmetry_hbond_refined0.122
r_bond_refined_d0.022
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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 Atoms12033
Nucleic Acid Atoms
Solvent Atoms1723
Heterogen Atoms529

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing