2NXZ

HIV-1 gp120 Envelope Glycoprotein (T257S, S334A, S375W) Complexed with CD4 and Antibody 17b


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G9Cpdb entry 1G9C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62987.5% PEG 4000, 8.5% MPD, 100 mM Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0359.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.915α = 90
b = 88.126β = 90
c = 197.685γ = 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
12.045092.20.1145.74.58047174195-3
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)
12.042.1268.20.5052.1

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 1G9C2.0435.388074266733357887.080.208210.206290.24425RANDOM25.41
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]
0.44-0.33-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.93
r_dihedral_angle_4_deg16.279
r_dihedral_angle_3_deg14.13
r_dihedral_angle_1_deg5.28
r_scangle_it1.803
r_scbond_it1.058
r_angle_refined_deg0.997
r_mcangle_it0.688
r_mcbond_it0.39
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.93
r_dihedral_angle_4_deg16.279
r_dihedral_angle_3_deg14.13
r_dihedral_angle_1_deg5.28
r_scangle_it1.803
r_scbond_it1.058
r_angle_refined_deg0.997
r_mcangle_it0.688
r_mcbond_it0.39
r_nbtor_refined0.32
r_symmetry_hbond_refined0.285
r_nbd_refined0.207
r_xyhbond_nbd_refined0.204
r_symmetry_vdw_refined0.162
r_chiral_restr0.063
r_bond_refined_d0.009
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 Atoms7105
Nucleic Acid Atoms
Solvent Atoms563
Heterogen Atoms229

Software

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