Evidence: native gel electrophoresis, isothermal titration calorimetry
Type
Name
Symmetry operation
Number
identity operation
1_555
1
NMR ensembles
Data
Criteria
Number of conformers (submitted / calculated)
10 / 100
10 structures for lowest energy
Representative
Model #1
lowest energy
-
Components
#1: RNA chain
VEGFAx1
Mass: 5215.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle)
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
1
1
anisotropic
1
2D NOESY
2
2
2
anisotropic
2
1H-13C HMQC
3
3
3
anisotropic
1
2D NOESY
-
Sample preparation
Details
Type
Solution-ID
Contents
Label
Solvent system
solution
1
1mMRNA, 100% D2O
D2O_NOESY_sample
100% D2O
solution
2
1 mM [U-13C] RNA, 100% D2O
HMQC_sample
100% D2O
solution
3
1mMRNA, 10%D2O90%H2O
H2O_NOESY_sample
10%D2O90%H2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
1mM
RNA
naturalabundance
1
1mM
RNA
[U-13C]
2
1mM
RNA
naturalabundance
3
Sample conditions
Conditions-ID
Ionic strength
Label
pH
Pressure (kPa)
Temperature (K)
1
50MMKCLmM
Condition_1
5.6
ambient
311K
2
50MMKCLmM
Condition_2
5.6
ambient
311K
3
50MMKCLmM
Condition_3
5.6
ambient
278K
-
NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker Ascend800
Bruker
Ascend800
800
1
Bruker UltraShield700Plus
Bruker
UltraShield700Plus
700
2
-
Processing
NMR software
Name
Version
Developer
Classification
NMRDraw
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
NMRViewJ
BruceA. Johnson
chemicalshiftassignment
CYANA
Guntert, MumenthalerandWuthrich
structurecalculation
X-PLOR NIH
3.1
Schwieters, Kuszewski, TjandraandClore
refinement
Refinement
Method: simulated annealing / Software ordinal: 3 Details: First round of structure calculation was conducted with distance and dihedral angle restraints only. Second round was performed with electrostatics using both high temperature annealing and ...Details: First round of structure calculation was conducted with distance and dihedral angle restraints only. Second round was performed with electrostatics using both high temperature annealing and low temperature annealing.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: 10 structures for lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10
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