5FYK

Crystal Structure at 3.7 A Resolution of Fully Glycosylated HIV-1 Clade B JR-FL SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122, 35O22 and VRC01


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4TVPPDB ENTRY 4TVP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.54.95% ISOPROPANOL, 8.25% PEG 3350, 0.2M AMMONIUM CITRATE PH 4.5
Crystal Properties
Matthews coefficientSolvent content
3.4864.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.78α = 90
b = 130.78β = 90
c = 314.62γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMAR2014-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

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
13.15086.20.077.763.7550012

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4TVP3.10742.8081.3931882165458.330.24880.24560.303
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_d15.555
f_angle_d1.059
f_chiral_restr0.041
f_bond_d0.005
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13259
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms1565

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling