4TVP

Crystal Structure of the HIV-1 BG505 SOSIP.664 Env Trimer Ectodomain, Comprising Atomic-Level Definition of Pre-Fusion gp120 and gp41, in Complex with Human Antibodies PGT122 and 35O22


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JY54JY5,4TOY,4J6R
experimental modelPDB 4TOY4JY5,4TOY,4J6R
experimental modelPDB 4J6R4JY5,4TOY,4J6R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529316% isopropanol, 5.32% PEG1500, 0.2M LiSO4, 0.1M Sodium acetate pH 5.5
Crystal Properties
Matthews coefficientSolvent content
4.4572.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.89α = 90
b = 128.89β = 90
c = 313.42γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HS2014-04-20MSINGLE 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
13.15073.411.33.839567
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.2127.81.113

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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 REPLACEMENTFREE R-VALUE4JY5,4TOY,4J6R3.140.7391.3829353144955.040.21520.21350.248
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_d8.717
f_angle_d0.575
f_chiral_restr0.023
f_plane_restr0.003
f_bond_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11344
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms807

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing