1W1X

Structure of Neuraminidase from English duck subtype N6 complexed with 30 mM sialic acid (NANA, Neu5Ac), crystal soaked for 3 hours at 277 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
2.550.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.993α = 90
b = 73.464β = 90.38
c = 107.413γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD1.2 METRE LONG SILICON SUBSTRATE, RHODIUM COATED2004-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.2SRSPX14.2

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
1233.7899.40.124.63.311203216.63
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)
122.11990.32.33.3

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 1V0Z233.7110620356341000.1670.1640.207RANDOM21.28
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]
-2.48-0.545.38-2.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.435
r_scangle_it4.497
r_scbond_it3.244
r_angle_refined_deg2.145
r_mcangle_it1.903
r_mcbond_it1.228
r_nbd_refined0.249
r_symmetry_vdw_refined0.249
r_chiral_restr0.176
r_symmetry_hbond_refined0.174
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.435
r_scangle_it4.497
r_scbond_it3.244
r_angle_refined_deg2.145
r_mcangle_it1.903
r_mcbond_it1.228
r_nbd_refined0.249
r_symmetry_vdw_refined0.249
r_chiral_restr0.176
r_symmetry_hbond_refined0.174
r_xyhbond_nbd_refined0.161
r_bond_refined_d0.028
r_gen_planes_refined0.012
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 Atoms1565
Heterogen Atoms525

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing