3CYE

Cyrstal structure of the native 1918 H1N1 neuraminidase from a crystal with lattice-translocation defects


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HTYPDB entry 2HTY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52950.16 M CALCIUM ACETATE; 0.08 M CACODYLATE; 14.4% PEG8000; 20% GLYCEROL, PH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.8356.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.728α = 90
b = 138.472β = 90
c = 117.86γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2006-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-21.00797SSRLBL9-2

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
11.655097.30.09322.24.2113144
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)
11.651.6876.40.5282.84405

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2HTY1.6544.86113058565297.130.1930.231RANDOM14.726
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]
-1.252.27-1.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.45
r_dihedral_angle_3_deg12.452
r_dihedral_angle_4_deg11.825
r_dihedral_angle_1_deg6.806
r_scangle_it2.602
r_scbond_it1.829
r_angle_refined_deg1.323
r_mcangle_it1.183
r_mcbond_it0.768
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.45
r_dihedral_angle_3_deg12.452
r_dihedral_angle_4_deg11.825
r_dihedral_angle_1_deg6.806
r_scangle_it2.602
r_scbond_it1.829
r_angle_refined_deg1.323
r_mcangle_it1.183
r_mcbond_it0.768
r_nbtor_refined0.301
r_nbd_refined0.222
r_symmetry_vdw_refined0.184
r_symmetry_hbond_refined0.16
r_xyhbond_nbd_refined0.138
r_chiral_restr0.09
r_metal_ion_refined0.089
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5926
Nucleic Acid Atoms
Solvent Atoms754
Heterogen Atoms154

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling