3TGT

Crystal structure of unliganded HIV-1 clade A/E strain 93TH057 gp120 core


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529314% PEG 1500, 12% PEG 400, 0.1M HEPES, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.3948.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.556α = 90
b = 66.944β = 90
c = 88.029γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2010-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1APS22-BM

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
11.95095.20.0840.07438.56.83246530907
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)
11.91.9386.50.6150.5552.15.5

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.924.5710.113182429250143791.910.1910.1890.2307
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]
10.722-4.9969-5.7251
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.937
f_angle_d1.198
f_chiral_restr0.069
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2677
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms155

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling