4QNP

Crystal structure of the 2009 pandemic H1N1 influenza virus neuraminidase with a neutralizing antibody


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4B7MPDB ENTRY 4B7M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.09 M malonic acid, 0.013 M ammonium citrate tribasic, 0.006 M succinic acid, 0.015 M DL-malic acid, 0.02 M sodium acetate, 0.025 M sodium formate, 0.008 M ammonium tartrate dibasic, 0.1 M HEPES/NaOH, 10% w/v PEG8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9357.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.29α = 90
b = 202.951β = 90
c = 143.968γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.847.85399.1522724857422
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.8799.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4B7M2.847.8524863346115245892.90.190.183180.181030.22379RANDOM48.269
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]
-0.10.12-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.61
r_dihedral_angle_3_deg17.025
r_dihedral_angle_4_deg16.354
r_dihedral_angle_1_deg7.34
r_long_range_B_refined6.407
r_long_range_B_other6.404
r_scangle_other4.429
r_mcangle_it3.958
r_mcangle_other3.958
r_scbond_it2.798
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.61
r_dihedral_angle_3_deg17.025
r_dihedral_angle_4_deg16.354
r_dihedral_angle_1_deg7.34
r_long_range_B_refined6.407
r_long_range_B_other6.404
r_scangle_other4.429
r_mcangle_it3.958
r_mcangle_other3.958
r_scbond_it2.798
r_scbond_other2.798
r_mcbond_it2.469
r_mcbond_other2.469
r_angle_refined_deg1.612
r_angle_other_deg0.957
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12635
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms116

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling