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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Experiment
1MFJ
3' Stem-Loop from Human U4 SNRNA
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
Download Files
FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
NMR Restraints (Text)
NMR Restraints (gz)
V2 NMR Restraints (gz)
SOLUTION NMR Experimental Data
Experimental Details
Sample Conditions
Sample Contents
1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chloride
Solvent
D2O
Ionic Strength
10 mM sodium phosphate & 50 mM NaCl
pH
6.4
Pressure
ambient
Temperature (K)
303
Experiment(s):
2D NOESY, DQF-COSY, 2D TOCSY, natural abundance 13C-HMQC
Sample Contents
1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chloride
Solvent
90% H2O/10% D2O
Ionic Strength
10 mM sodium phosphate & 50 mM NaCl
pH
6.4
Pressure
ambient
Temperature (K)
293
Experiment(s):
2D NOESY
Spectrometer Information
Manufacturer
Model
Field Strength
Varian
INOVA
600.0
NMR Refinement
Method
complete relaxation matrix; random error analysis of NOE; torsion angle dynamics; simulated annealing using Metropolis Monte Carlo; restrained minimization
Details
Structures are based on 200 distance restraints, of which 140 are quantitative bounds for nonexchangeable protons calculated with MARDIGRAS, 56 are upper bounds for exchangeable protons, and 4 are hydrogen bond restraints.
NMR Ensemble Information
Conformer Selection Criteria
Lowest total energy (a weighted sum of conformational energy and restraint energy).
Conformers Calculated Total Number
15
Conformers Submitted Total Number
10
Representative Model Choice Rationale
1
lowest total energy
Additional NMR Experimental Information
1
This structure was determined using standard 2D homonuclear techniques and complete relaxation matrix analysis of NOE intensities.
Computation: NMR Software
#
Classification
Software Name
Author
1
collection version: 6.1
VNMR
Varian Associates, Inc.
2
processing version: 2.1
NMRPipe
Delaglio
3
data analysis version: 3.0
Sparky
Goddard & Kneller
4
iterative matrix relaxation version: 3.2
MARDIGRAS
Borgias et al.
5
refinement version: 1.5
DYANA
Guentert
6
refinement
miniCarlo
Ulyanov et al.