5FYL

Crystal Structure at 3.7 A Resolution of Fully Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122 and 35O22


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.50.18 M LI2SO4, 4.79% PEG 1500, 14.4% ISOPROPANOL, 10 MM YTTRIUM CHLORIDE, 0.09 M SODIUM ACETATE PH 5.5
Crystal Properties
Matthews coefficientSolvent content
4.4872.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.78α = 90
b = 129.78β = 90
c = 313.06γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCH2014-08-23MSINGLE 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
13.15085.10.064.825536172

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 4TVP3.140.9981.3631517171058.470.25370.25030.3072
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_d14.97
f_angle_d0.961
f_chiral_restr0.036
f_bond_d0.005
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11344
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms1374

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling