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An Information Portal to 105097 Biological Macromolecular Structures

SOLUTION NMR
Materials and Methods page
2LXC
  •   NMR Eperiment Details Hide
    Representative Model Choice Rationale
    lowest energy  
     
    Spectrometer Info
    Field Strength 800.0
    Manufacturer Bruker
    Model Avance
    Field Strength 600.0
    Manufacturer Varian
    Model INOVA
     
    Sample Conditions
    IDs solution ID:1 condition ID:1
    Sample Contents 1 mM Get5, 2 mM [U-100% 13C; U-100% 15N] Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 0
    pH 6.1
    Pressure ambient
    Temperature 310
    IDs solution ID:2 condition ID:1
    Sample Contents 1 mM Get5, 2 mM [U-100% 13C; U-100% 15N] Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide, 3.5 % polyacrylamide, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 0
    pH 6.1
    Pressure ambient
    Temperature 310
    IDs solution ID:3 condition ID:1
    Sample Contents 1 mM [U-100% 13C; U-100% 15N] Get5, 2 mM Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 0
    pH 6.1
    Pressure ambient
    Temperature 310
    IDs solution ID:4 condition ID:1
    Sample Contents 1 mM [U-100% 13C; U-100% 15N] Get5, 2 mM Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide, 3.5 % polyacrylamide, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 0
    pH 6.1
    Pressure ambient
    Temperature 310
     
     
  •   NMR Refinement Information Hide
    Refinement
    Method simulated annealing, experimentally driven docking
    Details STRUCTURES OF ASYMMETRICALLY LABELED COMPLEX (SAMPLE_1 AND SAMPLE_3) WERE USED TO DETERMINE THE SEPERATE STRUCTURES OF GET5 OR SGT2, IN THEIR COMPLEX STATES. STRUCTURES ARE REFINED IN EXPLICIT WATER. AMBIGUOUS INTERACTION RESTRAINTS, RESIDUAL DIPOLAR COUPLINGS AND INTERMOLECULAR NOES WERE USED TO DOCK THE STRUCTURES OF GET5 AND SGT2, DETERMINED IN THEIR COMPLEX STATES. STRUCTURES ARE SELECTED FROM THE BEST SCORING CLUSTER BY HADDOCK SCORES AND REFINED IN WATER.
     
  •   NMR Ensemble Information Hide
    Ensemble
    Conformer Selection Criteria structures with the lowest energy
    Conformers Calculated Total Number 200
    Conformers Submitted Total Number 10
     
  •   NMR Experimental Information Hide
    Experiment
    IDs experiment ID:1 solution ID:1 conditons ID:1
    Type 2D 1H-15N HSQC
    IDs experiment ID:10 solution ID:3 conditons ID:1
    Type 3D HCCH-TOCSY
    IDs experiment ID:11 solution ID:3 conditons ID:1
    Type 3D 1H-15N NOESY
    IDs experiment ID:12 solution ID:3 conditons ID:1
    Type 3D 1H-13C NOESY aliphatic
    IDs experiment ID:13 solution ID:2 conditons ID:1
    Type 2D 1H-15N HSQC
    IDs experiment ID:14 solution ID:4 conditons ID:1
    Type 2D 1H-15N HSQC
    IDs experiment ID:2 solution ID:1 conditons ID:1
    Type 3D 1H-15N NOESY
    IDs experiment ID:3 solution ID:1 conditons ID:1
    Type 3D 1H-15N TOCSY
    IDs experiment ID:4 solution ID:1 conditons ID:1
    Type 2D 1H-13C HSQC aliphatic
    IDs experiment ID:5 solution ID:1 conditons ID:1
    Type 2D 1H-13C HSQC aromatic
    IDs experiment ID:6 solution ID:3 conditons ID:1
    Type 2D 1H-15N HSQC
    IDs experiment ID:7 solution ID:3 conditons ID:1
    Type 3D HNCACB
    IDs experiment ID:8 solution ID:3 conditons ID:1
    Type 3D HNCO
    IDs experiment ID:9 solution ID:3 conditons ID:1
    Type 3D (H)CCH-TOCSY
     
  •   Software and Computing Hide
    NMR Software
    Authors Zweckstetter and Bax
    Classification data analysis
    Software Name PALES
    Authors Bruker Biospin
    Classification collection
    Software Name TOPSPIN
    Authors Alexandre Bonvin
    Classification structure solution
    Software Name HADDOCK 2.1
    Authors Linge, O'Donoghue and Nilges
    Classification refinement
    Software Name ARIA 2.3
    Authors Linge, O'Donoghue and Nilges
    Classification structure solution
    Software Name ARIA 2.3
    Authors Cornilescu, Delaglio and Bax
    Classification data analysis
    Software Name TALOS+
    Authors Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
    Classification processing
    Software Name NMRPipe
    Authors CCPN
    Classification chemical shift assignment
    Software Name Analysis
    Authors Varian
    Classification collection
    Software Name VNMRJ