6Q23

Crystal structure of human 1G01 Fab in complex with influenza virus neuraminidase from A/California/04/2009 (H1N1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NSS3NSS, 5ITB, 4FQL
experimental modelPDB 5ITB3NSS, 5ITB, 4FQL
experimental modelPDB 4FQL3NSS, 5ITB, 4FQL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 M Tris, pH 8.5, 10% (v/v) glycerol, 20% (w/v) PEG300, 5% (w/v) PEG8000
Crystal Properties
Matthews coefficientSolvent content
3.4564.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.594α = 90
b = 234.985β = 106.4
c = 106.275γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03309APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rpim I (All)CC (Half)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
13.2743.391.90.180.120.9524.52.77021453
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.273.3873.10.570.430.8761.12.2

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 REPLACEMENTTHROUGHOUT3NSS, 5ITB, 4FQL3.2743.366845335190.430.198410.19630.24078RANDOM57.757
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]
-44.99-1.5442.932.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.598
r_dihedral_angle_4_deg15.762
r_dihedral_angle_3_deg15.586
r_long_range_B_refined14.546
r_long_range_B_other14.546
r_mcangle_it8.599
r_mcangle_other8.599
r_scangle_other7.967
r_dihedral_angle_1_deg6.963
r_mcbond_it5.476
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.598
r_dihedral_angle_4_deg15.762
r_dihedral_angle_3_deg15.586
r_long_range_B_refined14.546
r_long_range_B_other14.546
r_mcangle_it8.599
r_mcangle_other8.599
r_scangle_other7.967
r_dihedral_angle_1_deg6.963
r_mcbond_it5.476
r_mcbond_other5.476
r_scbond_it5.107
r_scbond_other5.107
r_angle_refined_deg1.384
r_angle_other_deg1.342
r_chiral_restr0.055
r_bond_refined_d0.008
r_gen_planes_refined0.006
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25420
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms121

Software

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