2NY5

HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M) 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 DROP5.62989.2% PEG 4000, 9.5% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0659.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.262α = 90
b = 87.643β = 90
c = 197.334γ = 90
Symmetry
Space GroupP 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2003-10-13MSINGLE 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
12.55084.90.1639.23.94421037534-3
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)
12.52.5962.90.4782.7

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 1GC12.548.974488734804182881.610.20070.197920.25488RANDOM39.921
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]
-0.070.030.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.282
r_dihedral_angle_4_deg16.074
r_dihedral_angle_3_deg14.854
r_dihedral_angle_1_deg4.683
r_angle_refined_deg0.883
r_mcangle_it0.799
r_scangle_it0.612
r_mcbond_it0.458
r_scbond_it0.377
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.282
r_dihedral_angle_4_deg16.074
r_dihedral_angle_3_deg14.854
r_dihedral_angle_1_deg4.683
r_angle_refined_deg0.883
r_mcangle_it0.799
r_scangle_it0.612
r_mcbond_it0.458
r_scbond_it0.377
r_nbtor_refined0.323
r_xyhbond_nbd_refined0.246
r_nbd_refined0.22
r_symmetry_hbond_refined0.208
r_symmetry_vdw_refined0.176
r_chiral_restr0.056
r_bond_refined_d0.006
r_gen_planes_refined0.002
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 Atoms7078
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms149

Software

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