2BF1

Structure of an unliganded and fully-glycosylated SIV gp120 envelope glycoprotein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15293PROTEIN WAS CRYSTALLIZED FROM 15% PEG 6000, 100 MM SODIUM CITRATE, PH 5.0 AND 8% PEG 400 AT 20 DEGREES C.
Crystal Properties
Matthews coefficientSolvent content
3.9868.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.048α = 90
b = 108.048β = 90
c = 117.701γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDRH-COATED SI MIRROR2002-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F1CHESSF1

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
1426980.08124.5100402141.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
144.0994.30.821.34

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRASTHROUGHOUT4265842279980.3850.3850.38840.3880.405RANDOM128.8
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]
0.010.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.267
r_dihedral_angle_3_deg24.209
r_dihedral_angle_4_deg18.61
r_dihedral_angle_1_deg8.116
r_angle_refined_deg2.067
r_symmetry_vdw_refined0.368
r_nbtor_refined0.344
r_nbd_refined0.341
r_xyhbond_nbd_refined0.268
r_symmetry_hbond_refined0.194
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2471
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms615

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
REFMACrefinement