4CPY

Structure of the Neuraminidase from the B/Lyon/CHU/15.216/2011 virus in complex with Oseltamivir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CPOPDB ENTRY 4CPO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
125% PEG 1500, 0.1M SUCCINIC ACID PH 9.0
Crystal Properties
Matthews coefficientSolvent content
3.9568.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.094α = 90
b = 160.094β = 90
c = 89.8γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.845.2699.60.111.64.5121778214.7
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)
11.81.8399.90.522.24.3

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 4CPO1.845.26115551619399.550.172330.1720.17858RANDOM16.233
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]
1.191.19-2.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.808
r_dihedral_angle_3_deg13.231
r_dihedral_angle_4_deg10.179
r_dihedral_angle_1_deg6.85
r_angle_refined_deg1.346
r_mcangle_it0.794
r_angle_other_deg0.766
r_scbond_it0.724
r_mcbond_it0.47
r_mcbond_other0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.808
r_dihedral_angle_3_deg13.231
r_dihedral_angle_4_deg10.179
r_dihedral_angle_1_deg6.85
r_angle_refined_deg1.346
r_mcangle_it0.794
r_angle_other_deg0.766
r_scbond_it0.724
r_mcbond_it0.47
r_mcbond_other0.47
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms6030
Nucleic Acid Atoms
Solvent Atoms703
Heterogen Atoms194

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing