Experiment: 2MJZ

Capsid model of M13 bacteriophage virus from Magic-angle spinning NMR and Rosetta modeling

SOLID-STATE NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NCA	12 mg [U-99% 13C; U-99% 15N] M13 bacteriophage		5	8	ambient	288
2	2D NCO	12 mg [U-99% 13C; U-99% 15N] M13 bacteriophage		5	8	ambient	288
3	2D DARR	12 mg [U-99% 13C; U-99% 15N] M13 bacteriophage		5	8	ambient	288
4	2D CORD	8 mg [2-13C, 99%]- glycerol, [15N-U, 99%], [13C,99%] Sodium bicarbonate M13 bacteriophage		5	8	ambient	288
5	2D CORD	10 mg [1,3-13C2, 99%]- glycerol, [15N-U, 99%] M13 bacteriophage		5	8	ambient	288
6	2D RFDR	12 mg [U-99% 13C; U-99% 15N] M13 bacteriophage		5	8	ambient	288
7	3D NCOCX	12 mg [U-99% 13C; U-99% 15N] M13 bacteriophage		5	8	ambient	288
8	3D NCACX	12 mg [U-99% 13C; U-99% 15N] M13 bacteriophage		5	8	ambient	288
9	2D DARR	8 mg [2-13C, 99%]- glycerol, [15N-U, 99%], [13C,99%] Sodium bicarbonate M13 bacteriophage		5	8	ambient	288
10	2D DARR	10 mg [1,3-13C2, 99%]- glycerol, [15N-U, 99%] M13 bacteriophage		5	8	ambient	288

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	600

NMR Refinement
Method	Details	Software
Fold-and-dock	magic angle spinning, backbone fragment-based Monte Carlo trials followed by combinatorial sidechain packing	TopSpin

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	5000
Conformers Submitted Total Number	3
Representative Model	1 (lowest energy)

Additional NMR Experimental Information
Details	IN THE PDB FILE THE 35 SUBUNITS MODELED ARE REPRESENTED AS CHAINS NUMBERED FROM A-Z, a-i. THE NOTATION WE USED IN THE PAPER FOR DESCRIBING THE CAPSID ARRANGEMENT IS BASED ON THE PENTAMER SYMMETRY; EACH SUBUNIT PNM IS GIVEN TWO INDICES, WHERE THE INDEX N INDICATES THE PENTAMER NUMBER (N BETWEEN 1-7 WHERE N=1 CORRESPONDS TO THE C-TERMINAL PART) AND M INDICATES THE IDENTITY OF THE SUBUNIT WITHIN EACH PENTAMER(M=1-5). THE TRANSFORMATION FROM THE PAPER'S NOTATION TO THE RESPECTIVE PDB CHAINS IS AS FOLLOWS: P11 J P12 K P13 L P14 M P15 N P21 O P22 P P23 Q P24 R P25 S P31 T P32 U P33 V P34 W P35 X P41 Y P42 Z P43 a P44 b P45 c P51 d P52 e P53 f P54 g P55 h P61 i P62 A P63 B P64 C P65 D P71 E P72 F P73 G P74 H P75 I

Additional NMR Experimental Information

Details

IN THE PDB FILE THE 35 SUBUNITS MODELED ARE REPRESENTED AS CHAINS NUMBERED FROM A-Z, a-i. THE NOTATION WE USED IN THE PAPER FOR DESCRIBING THE CAPSID ARRANGEMENT IS BASED ON THE PENTAMER SYMMETRY; EACH SUBUNIT PNM IS GIVEN TWO INDICES, WHERE THE INDEX N INDICATES THE PENTAMER NUMBER (N BETWEEN 1-7 WHERE N=1 CORRESPONDS TO THE C-TERMINAL PART) AND M INDICATES THE IDENTITY OF THE SUBUNIT WITHIN EACH PENTAMER(M=1-5). THE TRANSFORMATION FROM THE PAPER'S NOTATION TO THE RESPECTIVE PDB CHAINS IS AS FOLLOWS: P11 J P12 K P13 L P14 M P15 N P21 O P22 P P23 Q P24 R P25 S P31 T P32 U P33 V P34 W P35 X P41 Y P42 Z P43 a P44 b P45 c P51 d P52 e P53 f P54 g P55 h P61 i P62 A P63 B P64 C P65 D P71 E P72 F P73 G P74 H P75 I

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	TopSpin	2.1	Bruker Biospin
2	data analysis	TopSpin	2.1	Bruker Biospin
3	processing	NMRPipe	2012.090.12.09	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	chemical shift assignment	Sparky	3.113	Goddard
5	data analysis	Sparky	3.113	Goddard
6	peak picking	Sparky	3.113	Goddard
7	refinement	Rosetta		Shen, Vernon, Baker and Bax

2MJZ | pdb_00002mjz

Capsid model of M13 bacteriophage virus from Magic-angle spinning NMR and Rosetta modeling