1QKH

SOLUTION STRUCTURE OF THE RIBOSOMAL PROTEIN S19 FROM THERMUS THERMOPHILUS

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	HNCA	90% WATER/10% D2O		0.250 M	6.5	1 atm	303
2	HN(CO)CA	90% WATER/10% D2O		0.250 M	6.5	1 atm	303
3	CBCANH	90% WATER/10% D2O		0.250 M	6.5	1 atm	303
4	CBCA(CO)NH	90% WATER/10% D2O		0.250 M	6.5	1 atm	303
5	C(CO)NH-TOCSY	90% WATER/10% D2O		0.250 M	6.5	1 atm	303
6	HCCH-TOCSY	90% WATER/10% D2O		0.250 M	6.5	1 atm	303
7	(HB)CB(CGCD)HD	90% WATER/10% D2O		0.250 M	6.5	1 atm	303
8	(HB)CB(CGCDCE)HE	90% WATER/10% D2O		0.250 M	6.5	1 atm	303
9	15N-EDITED NOESY-HSQC	90% WATER/10% D2O		0.250 M	6.5	1 atm	303
10	15N-EDITED TOCSY-HSQC	90% WATER/10% D2O		0.250 M	6.5	1 atm	303
11	3D HNHA	90% WATER/10% D2O		0.250 M	6.5	1 atm	303
12	2D NOESY	90% WATER/10% D2O		0.250 M	6.5	1 atm	303
13	2D TOCSY	90% WATER/10% D2O		0.250 M	6.5	1 atm	303

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	500
2	Varian	INOVA	600
3	Varian	INOVA	800

NMR Refinement
Method	Details	Software
simulated annealing	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.	X-PLOR

NMR Ensemble Information
Conformer Selection Criteria	CUMULATIVE RMSD OF STRUCTURES SORTED AFTER TOTAL ENERGY
Conformers Calculated Total Number	50
Conformers Submitted Total Number	21

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	X-PLOR	3.851	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 FROM IDEAL GEOMETRY BONDS 0.0045 A 0.0041 A ANGLES 0.71 DEG 0.66 DEG IMPROPERS 0.54 DEG 0.49 DEG
2	structure solution	VNMR	5.3
3	structure solution	PRONTO (VERSION 970523)	970523)
4	structure solution	X-PLOR (VERSION 3.851)	3.851)
5	structure solution	MOLMOL (VERSION 2.6)	2.6)
6	structure solution	PROCHECK-NMR