4NM8

Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza hemagglutinin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FNKPDB ENTRY 4FNK, 4NM4
experimental modelPDB 4NM4PDB ENTRY 4FNK, 4NM4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52772.2 M ammonium sulfate, 0.1 M sodium acetate pH 5.5, 3% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3963.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 241.491α = 90
b = 142.355β = 133.46
c = 170.725γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77PIXELPSI PILATUS 6M2012-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97950SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
145097.70.2010.2016.46.83462234622-392.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
144.290.80.8260.8262.26.54271

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4FNK, 4NM44.004143.8211.9934531173097.370.24230.23970.2924RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.276
f_angle_d1.227
f_chiral_restr0.078
f_bond_d0.006
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21392
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms280

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling