2MJZ
Capsid model of M13 bacteriophage virus from Magic-angle spinning NMR and Rosetta modeling
SOLID-STATE NMR
NMR Experiment | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | Avance-III | 600 |
NMR Refinement | ||
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Method | Details | Software |
Fold-and-dock | magic angle spinning, backbone fragment-based Monte Carlo trials followed by combinatorial sidechain packing | TOPSPIN |
NMR Ensemble Information | |
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Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 5000 |
Conformers Submitted Total Number | 3 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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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 | ||||
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# | 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 |