structures with the least restraint violations,structures with the lowest energy
Representative
Model #1
closest to the average
-
Components
#1: RNA chain
D5-PLRNARIBOZYMEDOMAIN
Mass: 11009.607 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: RNA was synthesized by in vitro transcription with T7 RNA polymerase'
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Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
3
2D NOESY
2
2
3
2D TOCSY
2
3
1
3D 13C-separated NOESY
1
4
1
3D 15N-separated NOESY
3
5
1
3D 1H-13C-1H (H)CCHTOCSY
3
6
1
3D 1H-13C-1H (H)CCHCOSY
3
7
1
3D 1H-13C-1H (H)CCHCOSYTROSY
3
8
1
3DHCCNH
2
9
2
3D 13C-separated ROESY
4
10
1
13C/15N HSQC
4
11
1
13C/15N TROSY
NMR details
Text: The structure was determined using a battery of standard homonuclear and recently optimized triple-resonance NMR experiments
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1 mM fully 13C/15N A,C,G,U labeled D5-PL, 100 mM KCl, 10 mM phosphate, 0-10 mM MgCl2, 92% H2O and 8% D2O or 99.999% D2O
92% H2Oand8% D2Oor99.999% D2O
2
1 mM A-13C/15N Uracil labeled D5-PL, 100 mM KCl, 10 mM phosphate buffer, 0-10 mM MgCl2, 92% H2O and 8% D2O or 99.999% D2O
92% H2Oand8% D2Oor99.999% D2O
3
1 mM unlabeled D5-PL, 100 mM KCl, 10 mM phosphate buffer, 0-10 mM MgCl2, 92% H2O and 8% D2O or 99.999% D2O
92% H2Oand8% D2Oor99.999% D2O
Sample conditions
Conditions-ID
Ionic strength
pH
Temperature (K)
1
100mMKCl
6.5
278K
2
100mMKCl
6.5
298K
3
100mMKCl
6.5
308K
4
100mMKCl
6.5
318K
-
NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Varian INOVA
Varian
INOVA
500
1
Varian INOVA
Varian
INOVA
600
2
Bruker AVANCE
Bruker
AVANCE
600
3
Bruker AVANCE
Bruker
AVANCE
800
4
-
Processing
NMR software
Name
Version
Developer
Classification
NMRPipe
2.1
Delaglio, Bax
processing
Sparky
3
Goddard & Kneller
dataanalysis
CNS
1.1
Brunger
structuresolution
CNS
1.1
Brunger
refinement
Refinement
Method: TORSION ANGLE MOLECULAR DYNAMICS CARTESIAN SPACE SIMULATED ANNEALING RESIDUAL DIPOLAR COUPLINGS REFINEMENT Software ordinal: 1 Details: STRUCTURES BASED ON 549 NOE-DERIVED DISTANCE RESTRAINTS, 304 DIHEDRAL RESTRAINTS, 60 HYDROGEN BOND RESTRAINTS, AND 37 RESIDUAL DIPOLAR COUPLING RESTRAINTS
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 10
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