3H01

Structure of the C-terminal Domain of a Putative HIV-1 gp41 Fusion Intermediate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GWOPDB ENTRY 3GWO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52952.8M 1,6-hexanediol, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3347.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.967α = 90
b = 33.967β = 90
c = 191.331γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.9795NSLSX4A

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
11.729.4198.90.06116.25.3149061490620.8
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)
11.71.7698.80.14210.54.51422

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3GWO1.729.41149061490675298.90.206470.206470.205280.22805RANDOM23.359
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]
0.330.160.33-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.16
r_dihedral_angle_4_deg20.524
r_dihedral_angle_3_deg12.421
r_scangle_it3.766
r_dihedral_angle_1_deg3.363
r_scbond_it2.764
r_mcangle_it1.536
r_angle_refined_deg1.34
r_mcbond_it0.972
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.16
r_dihedral_angle_4_deg20.524
r_dihedral_angle_3_deg12.421
r_scangle_it3.766
r_dihedral_angle_1_deg3.363
r_scbond_it2.764
r_mcangle_it1.536
r_angle_refined_deg1.34
r_mcbond_it0.972
r_nbtor_refined0.303
r_symmetry_vdw_refined0.219
r_nbd_refined0.199
r_xyhbond_nbd_refined0.142
r_chiral_restr0.096
r_symmetry_hbond_refined0.084
r_bond_refined_d0.018
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms862
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms64

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling