1MZI

Solution ensemble structures of HIV-1 gp41 2F5 mAb epitope


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESY1.5mM peptide, 50mM phosphate buffer, pH 6.595% H2O/5% D2O50mM phosphate buffer6.5ambient278
22D TOCSY1.5mM peptide, 50mM phosphate buffer, pH 6.595% H2O/5% D2O50mM phosphate buffer6.5ambient278
3PE-COSY1.5mM peptide, 50mM phosphate buffer, pH 6.595% H2O/5% D2O50mM phosphate buffer6.5ambient278
4HSQC (1H-13C)-Dipsi-2(1H)1.5mM peptide, 50mM phosphate buffer, pH 6.595% H2O/5% D2O50mM phosphate buffer6.5ambient278
5HMQC (1H-15N) jr1.5mM peptide, 50mM phosphate buffer, pH 6.595% H2O/5% D2O50mM phosphate buffer6.5ambient278
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerDRX600
2BrukerDRX500
NMR Refinement
MethodDetailsSoftware
Ensemble generation with MEDUSA, Clustering analysis with NMRCLUST, Statistical analysis of the ensemble with NAMFISNMRPipe
NMR Ensemble Information
Conformer Selection CriteriaBase set ensemble representative of the conformational space experimentally allowed
Conformers Calculated Total Number6400
Conformers Submitted Total Number81
Additional NMR Experimental Information
DetailsDistance restraints were determined using NOESY build-up curves. The coupling constants were determined using phase sensitive COSY and TOCSY experiments. E threshold cutoff and deltaE allowance for MEDUSA were 600 and 100 kCal/mol respectively Clustering was performed with a cutoff of 1.0Angstrom A conformer was defined as different if either phi or psi angle for at least one aminoacid was differing by >15 degrees
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1data analysisNMRPipe2001Delaglio, F.
2data analysisNMRView2001Johnson, B.
3refinementDGIIMSIMSI, Inc
4refinementNAMFIS1.0Cicero D.
5refinementMEDUSAin homeBrushweiler R.
6refinementNMRCLUST1.2Kelley