2NY4

HIV-1 gp120 Envelope Glycoprotein (K231C, T257S, E268C, S334A, S375W) 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 DROP5.62987.0% PEG 8000, 8.0% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9658.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.963α = 90
b = 87.957β = 90
c = 196.176γ = 90
Symmetry
Space GroupP 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 225 mm2003-02-13MSINGLE 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
125097.90.1256.56.18376982010-3
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)
122.0787.50.4443.8

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 1GC1242.918370474827398994.160.204070.202110.24072RANDOM32.662
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]
-0.110.090.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.658
r_dihedral_angle_4_deg15.935
r_dihedral_angle_3_deg13.264
r_dihedral_angle_1_deg5.138
r_scangle_it1.806
r_scbond_it1.056
r_angle_refined_deg0.935
r_mcangle_it0.727
r_mcbond_it0.412
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.658
r_dihedral_angle_4_deg15.935
r_dihedral_angle_3_deg13.264
r_dihedral_angle_1_deg5.138
r_scangle_it1.806
r_scbond_it1.056
r_angle_refined_deg0.935
r_mcangle_it0.727
r_mcbond_it0.412
r_nbtor_refined0.32
r_symmetry_hbond_refined0.223
r_nbd_refined0.208
r_xyhbond_nbd_refined0.205
r_symmetry_vdw_refined0.174
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 Atoms7099
Nucleic Acid Atoms
Solvent Atoms512
Heterogen Atoms213

Software

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