6MCO

Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P23 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4R264R26, 5CEZ
experimental modelPDB 5CEZ4R26, 5CEZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.150.1M HEPES (pH 7.0), 8% PEG8000
Crystal Properties
Matthews coefficientSolvent content
4.8674.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 212.326α = 90
b = 212.326β = 90
c = 212.326γ = 90
Symmetry
Space GroupP 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.03315APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.550.0461000.10.8410.137.539580
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.61000.39130.6

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-VALUE4R26, 5CEZ3.52650.0461.3339463195199.70.3070.30610.3223
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_d15.855
f_angle_d0.909
f_chiral_restr0.056
f_plane_restr0.015
f_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11417
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms851

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data scaling
PHENIXmodel building
HKL-2000data reduction
PHASERphasing