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An Information Portal to 105339 Biological Macromolecular Structures

SOLUTION NMR
Materials and Methods page
1QKH
  •   NMR Eperiment Details Hide
    Spectrometer Info
    Field Strength 800.0
    Field Strength 600.0
    Field Strength 500.0
    Manufacturer VARIAN
    Model UNITY INOVA
     
    Sample Conditions
    IDs solution ID:1 condition ID:1
    Sample Contents 90% WATER/10% D2O
    Ionic Strength 0.250 M
    pH 6.5
    Pressure 1
    Pressure Units ATM
    Temperature 303
     
     
  •   NMR Refinement Information Hide
    Refinement
    Method SIMULATED ANNEALING
    Details THE STRUCTURE WAS DETERMINED USING 1104 DISTANCE RESTRAINTS, 42 DIHEDRAL ANGLE RESTRAINTS AND 14 HYDROGEN BOND RESTRAINTS. 50 STRUCTURES WERE CALCULATED AND REFINED USING AN AB INITIO SIMULATED ANNEALING PROTOCOL FOR X- PLOR AND THEN REFINED IN TWO STEPS. AN R-6 AVERAGING PROTOCOL WAS USED FOR NON-STEREOSPECIFICALLY ASSIGNED PROTONS [1]. DURING THE SIMULATED ANNEALING STEP AND THE FIRST REFINEMENT STEP ONLY THE REPULSIVE PART OF THE VAN DER WAALS INTERACTION WAS INCLUDED. IN THE SECOND REFINEMENT STEP THE VAN DER WAALS INTERACTION WAS PARAMETERIZED USING A LENNARD-JONES POTENTIAL INCLUDING THE ATTRACTIVE PART. 21 STRUCTURES WERE SELECTED ON THE BASIS OF CUMULATIVE RMSD VALUES OF STRUCTURES, ORDERED AFTER OVERALL ENERGY, AND RAMACHANDRAN BEHAVIOR FOR REGIONS WITH LOW RESTRAINT DENSITIES. [1] BRUNGER, A. T., CLORE, G. M., GRONENBORN, A. M. & KARPLUS, M. (1986). THREE-DIMENSIONAL STRUCTURE OF PROTEINS DETERMINED BY MOLECULAR DYNAMICS WITH INTERPROTON DISTANCE RESTRAINTS: APPLICATION TO CRAMBIN. PROC NATL ACAD SCI USA 83, 3801-3805. OTHER DETAILS OF STRUCTURE REFINEMENT CAN BE FOUND IN THE JRNL CITATION.
     
  •   NMR Ensemble Information Hide
    Ensemble
    Conformer Selection Criteria CUMULATIVE RMSD OF STRUCTURES SORTED AFTER TOTAL ENERGY
    Conformers Calculated Total Number 50
    Conformers Submitted Total Number 21
     
  •   NMR Experimental Information Hide
    Experiment
    IDs experiment ID:1 solution ID:1 conditons ID:1
    Type HNCA
    IDs experiment ID:10 solution ID:1 conditons ID:1
    Type 15N-EDITED TOCSY-HSQC
    IDs experiment ID:11 solution ID:1 conditons ID:1
    Type 3D HNHA
    IDs experiment ID:12 solution ID:1 conditons ID:1
    Type 2D NOESY
    IDs experiment ID:13 solution ID:1 conditons ID:1
    Type 2D TOCSY
    IDs experiment ID:2 solution ID:1 conditons ID:1
    Type HN(CO)CA
    IDs experiment ID:3 solution ID:1 conditons ID:1
    Type CBCANH
    IDs experiment ID:4 solution ID:1 conditons ID:1
    Type CBCA(CO)NH
    IDs experiment ID:5 solution ID:1 conditons ID:1
    Type C(CO)NH-TOCSY
    IDs experiment ID:6 solution ID:1 conditons ID:1
    Type HCCH-TOCSY
    IDs experiment ID:7 solution ID:1 conditons ID:1
    Type (HB)CB(CGCD)HD
    IDs experiment ID:8 solution ID:1 conditons ID:1
    Type (HB)CB(CGCDCE)HE
    IDs experiment ID:9 solution ID:1 conditons ID:1
    Type 15N-EDITED NOESY-HSQC
     
  •   Software and Computing Hide
    NMR Software
    Classification structure solution
    Software Name PROCHECK-NMR
    Classification structure solution
    Software Name MOLMOL (VERSION 2.6)
    Classification structure solution
    Software Name X-PLOR (VERSION 3.851)
    Classification structure solution
    Software Name PRONTO (VERSION 970523)
    Classification structure solution
    Software Name VNMR 5.3
    Authors BRUNGER STRUCTURAL STATISTICS: 21 SA STRUCTURES SAAVEMIN[A] RMS DEVIATIONS FROM EXP. RESTRAINTS NOE DISTANCE RESTRAINTS (1104) 0.036 A 0.032 A DIHEDRAL ANGLE RESTRAINTS (42) 0.380 DEG 0.380 DEG DEVIATIONS FRO
    Classification refinement
    Software Name M IDEAL GEOMETRY BONDS 0.0045 A 0.0041 A ANGLES 0.71 DEG 0.66 DEG IMPROPERS 0.54 DEG 0.49 DEG DEG 0.49 DEG