1G9M

HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING 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 DROP6.4293VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0.0075% SEAPREP AGAROSE, PH 6.4 OVER A RESERVOIR OF 0.35 M NACL, 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, PH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
359

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.25α = 90
b = 88.11β = 90
c = 196.54γ = 90
Symmetry
Space GroupP 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEFUJI1996-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.97953NSLSX4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.22087.70.1450.1455.332.4713881056183-0.3517.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2866.30.3820.3822.11.64207

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHIS DEPOSIT IS THE REFINEMENT OF THE PREVIOUSLY DETERMINED 1GC1 STRUCTURETHROUGHOUTpdb entry 1gc12.2206358255781394687.70.26760.3299random31.5
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]
-8.2681.017.258
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d26.2
c_scangle_it3.13
c_mcangle_it2.94
c_scbond_it2.06
c_mcbond_it1.7
c_angle_deg1.1889
c_improper_angle_d0.87
c_bond_d0.0074
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7149
Nucleic Acid Atoms
Solvent Atoms953
Heterogen Atoms220

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement