2NY6

HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GC1pdb entry 1GC1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62988.3% PEG 8000, 7.4% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9858.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.31α = 90
b = 87.018β = 90
c = 196.078γ = 90
Symmetry
Space GroupP 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2005-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

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
12.85092.50.1514.83.43083828525-3
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)
12.82.9650.5812.6

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1GC12.842.373142223560118878.760.19590.191990.27577RANDOM51.499
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]
-4.32.122.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.956
r_dihedral_angle_3_deg16.702
r_dihedral_angle_4_deg14.507
r_dihedral_angle_1_deg5.283
r_mcangle_it2.281
r_scangle_it1.962
r_mcbond_it1.336
r_scbond_it1.245
r_angle_refined_deg1.032
r_nbtor_refined0.341
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.956
r_dihedral_angle_3_deg16.702
r_dihedral_angle_4_deg14.507
r_dihedral_angle_1_deg5.283
r_mcangle_it2.281
r_scangle_it1.962
r_mcbond_it1.336
r_scbond_it1.245
r_angle_refined_deg1.032
r_nbtor_refined0.341
r_symmetry_vdw_refined0.31
r_nbd_refined0.302
r_xyhbond_nbd_refined0.278
r_symmetry_hbond_refined0.258
r_chiral_restr0.079
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7082
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms135

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing