2KPV | pdb_00002kpv

NMR model of the first let-7 miRNA complementary site (LCS1) in 3'-UTR of lin-41 mRNA from C. elegans

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6	100% D2O	20	6.8	ambient	303
2	2D 15N-HSQC	2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-1, 10mM sodium phosphate-2, 20mM sodium chloride-3	95% H2O/5% D2O	20	6.8	ambient	278
3	2D 13C-HSQC	2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6	100% D2O	20	6.8	ambient	303
4	2D DQF-COSY	2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6	100% D2O	20	6.8	ambient	303
5	2D HNN-COSY	2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-1, 10mM sodium phosphate-2, 20mM sodium chloride-3	95% H2O/5% D2O	20	6.8	ambient	278
6	2D TOCSY	2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6	100% D2O	20	6.8	ambient	303
7	2D 1H-31P COSY	2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6	100% D2O	20	6.8	ambient	303
8	2D 15N-IPAP-HSQC	1mM [U-100% 13C; U-100% 15N] RNA (34-MER)-7, 10mM sodium phosphate-8, 20mM sodium chloride-9, 17mg/mL Pf1 phage-10	90% H2O/10% D2O	20	6.8	ambient	303
9	3D HCCH-TOCSY	2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6	100% D2O	20	6.8	ambient	303
10	3D HCCH-COSY	2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6	100% D2O	20	6.8	ambient	303
11	3D 13C-separated-NOESY	2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6	100% D2O	20	6.8	ambient	303

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	NMR system	800
2	Varian	NMR system	600

NMR Refinement
Method	Details	Software
simulated annealing, energy minimization	810 NOE-derived distance restraints, 138 torsion angle restraints, 52 residual dipolar coupling restraints, 32 hydrogen bond restraints and 24 planarity restraints.	Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy and least restraint violations
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber	9	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollm
2	data analysis	Felix	2002	Accelrys Software Inc.
3	processing	Felix	2002	Accelrys Software Inc.
4	data collection	VnmrJ	2.1B	Varian

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.