2NY2

HIV-1 gp120 Envelope Glycoprotein (T123C, T257S, S334A, S375W, 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 DROP5.62987.2% PEG 8000, 7.8% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9858.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.605α = 90
b = 88.024β = 90
c = 196.016γ = 90
Symmetry
Space GroupP 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2005-03-03MSINGLE 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
125099.30.0829.13.78437983788-3
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)
122.0794.40.3743.4

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 1GC1242.848446175855406294.620.195260.193790.22296RANDOM40.166
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]
-0.060.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.529
r_dihedral_angle_4_deg14.81
r_dihedral_angle_3_deg12.812
r_dihedral_angle_1_deg5.068
r_mcangle_it1.232
r_scangle_it0.969
r_angle_refined_deg0.911
r_mcbond_it0.715
r_scbond_it0.597
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.529
r_dihedral_angle_4_deg14.81
r_dihedral_angle_3_deg12.812
r_dihedral_angle_1_deg5.068
r_mcangle_it1.232
r_scangle_it0.969
r_angle_refined_deg0.911
r_mcbond_it0.715
r_scbond_it0.597
r_nbtor_refined0.319
r_symmetry_hbond_refined0.318
r_nbd_refined0.202
r_xyhbond_nbd_refined0.199
r_symmetry_vdw_refined0.144
r_chiral_restr0.059
r_bond_refined_d0.005
r_gen_planes_refined0.003
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 Atoms7084
Nucleic Acid Atoms
Solvent Atoms665
Heterogen Atoms193

Software

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