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BMRB: 16691

2KT9

Solution NMR Structure of Probable 30S Ribosomal Protein PSRP-3 (Ycf65-like protein) from Synechocystis sp. (strain PCC 6803), Northeast Structural Genomics Consortium Target Target SgR46

Authors

Liu, G., Janjua, J., Xiao, R., Buchwald, W.A., Ciccosanti, C., Belote, R.L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T.

Assembly

SgR46

Entity

1. SgR46 (polymer, Thiol state: not present), 116 monomers, 13300.80 Da Detail

MAASTVHTSF ILKVLWLDQN VAIAVDQIVG KGTSPLTSYF FWPRADAWQQ LKDELEAKHW IAEADRINVL NQATEVINFW QDLKNQNKQI SMAEAQGKFP EVVFSGSNLE HHHHHH

Formula weight

13300.8 Da

Source organism

Synechocystis sp. PCC 6803

Exptl. method

solution NMR

Refine. method

simulated annealing, distance geometry, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.7 %, Completeness: 83.8 %, Completeness (bb): 77.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.8 % (1166 of 1391)	90.8 % (650 of 716)	73.2 % (396 of 541)	89.6 % (120 of 134)
Backbone	77.7 % (536 of 690)	89.7 % (209 of 233)	66.3 % (228 of 344)	87.6 % (99 of 113)
Sidechain	90.2 % (733 of 813)	91.3 % (441 of 483)	87.7 % (271 of 309)	100.0 % (21 of 21)
Aromatic	73.1 % (117 of 160)	78.8 % (63 of 80)	65.3 % (49 of 75)	100.0 % (5 of 5)
Methyl	99.3 % (133 of 134)	100.0 % (67 of 67)	98.5 % (66 of 67)

1. SgR46

MAASTVHTSF ILKVLWLDQN VAIAVDQIVG KGTSPLTSYF FWPRADAWQQ LKDELEAKHW IAEADRINVL NQATEVINFW QDLKNQNKQI SMAEAQGKFP EVVFSGSNLE HHHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 1.1 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	SgR46	[U-100% 13C; U-100% 15N]	1.1 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 0.8 mM [10% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	SgR46	[U-10% 13C; U-100% 15N]	0.8 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 0.3 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	SgR46	[U-100% 13C; U-100% 15N]	0.3 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.28 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.28 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KT9, Strand ID: A Detail

Release date

2010-02-24

Related entities 1. SgR46, : 1 : 1 : 25 entities Detail

Interaction partners 1. SgR46, : 5 interactors Detail

More details for 5 interactors identified by 1 citations

Experiments performed 24 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 1.1 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	SgR46	[U-100% 13C; U-100% 15N]	1.1 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

2 2D 1H-13C HSQC aliphatic 927

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 1.1 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	SgR46	[U-100% 13C; U-100% 15N]	1.1 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 4.5, Details 0.3 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	SgR46	[U-100% 13C; U-100% 15N]	0.3 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

4 3D CBCA(CO)NH 816

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 4.5, Details 0.3 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	SgR46	[U-100% 13C; U-100% 15N]	0.3 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 4.5, Details 0.3 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	SgR46	[U-100% 13C; U-100% 15N]	0.3 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 1.1 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	SgR46	[U-100% 13C; U-100% 15N]	1.1 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

7 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 1.1 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	SgR46	[U-100% 13C; U-100% 15N]	1.1 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

8 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 0.8 mM [10% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	SgR46	[U-10% 13C; U-100% 15N]	0.8 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

9 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 4.5, Details 0.3 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	SgR46	[U-100% 13C; U-100% 15N]	0.3 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

10 3D HCCH-TOCSY 829

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 1.1 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	SgR46	[U-100% 13C; U-100% 15N]	1.1 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

11 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 1.1 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	SgR46	[U-100% 13C; U-100% 15N]	1.1 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

12 3D CBCA(CO)NH 819

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 4.5, Details 0.3 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	SgR46	[U-100% 13C; U-100% 15N]	0.3 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

13 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 4.5, Details 0.3 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	SgR46	[U-100% 13C; U-100% 15N]	0.3 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

14 3D HNCOCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 4.5, Details 0.3 mM [U-100% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	SgR46	[U-100% 13C; U-100% 15N]	0.3 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

15 3D 1H-15N NOESY 939

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 0.8 mM [10% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	SgR46	[U-10% 13C; U-100% 15N]	0.8 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

16 3D 1H-15N NOESY 940

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 0.8 mM [10% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	SgR46	[U-10% 13C; U-100% 15N]	0.8 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

17 1D T1

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 0.8 mM [10% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	SgR46	[U-10% 13C; U-100% 15N]	0.8 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

18 1D T2

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 0.8 mM [10% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	SgR46	[U-10% 13C; U-100% 15N]	0.8 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

19 3D 1H-13C arom TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 0.8 mM [10% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	SgR46	[U-10% 13C; U-100% 15N]	0.8 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

20 3D 1H-13C arom HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 0.8 mM [10% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	SgR46	[U-10% 13C; U-100% 15N]	0.8 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

21 3D HCCH-TOCSY 830

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 0.8 mM [10% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	SgR46	[U-10% 13C; U-100% 15N]	0.8 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

22 2D 1H-13C HSQC aliphatic 928

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 0.8 mM [10% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	SgR46	[U-10% 13C; U-100% 15N]	0.8 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

23 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 0.8 mM [10% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	SgR46	[U-10% 13C; U-100% 15N]	0.8 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

24 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.5, Details 0.8 mM [10% 13C; U-100% 15N] SR232, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	SgR46	[U-10% 13C; U-100% 15N]	0.8 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16691_2kt9.nef
Input source #2: Coordindates	2kt9.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MAASTVHTSFILKVLWLDQNVAIAVDQIVGKGTSPLTSYFFWPRADAWQQLKDELEAKHWIAEADRINVLNQATEVINFWQDLKNQNKQISMAEAQGKFP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAASTVHTSFILKVLWLDQNVAIAVDQIVGKGTSPLTSYFFWPRADAWQQLKDELEAKHWIAEADRINVLNQATEVINFWQDLKNQNKQISMAEAQGKFP

-------110------
EVVFSGSNLEHHHHHH
||||||||||||||||
EVVFSGSNLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	116	0	0	100.0

Content subtype: combined_16691_2kt9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1139		93.1 (chain: A, length: 116)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3434 (1)	noe	90.5 (chain: A, length: 116)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	62 (1)	hbond	44.8 (chain: A, length: 116)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	148 (148)	.	80.2 (chain: A, length: 116)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 93.1%
- Total number of assignments
  - ¹H chemical shifts: 649
  - ¹³C chemical shifts: 373
  - ¹⁵N chemical shifts: 117
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
37	THR	HG1	5.36

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	716	648	90.5
¹³C chemical shifts	541	373	68.9
¹⁵N chemical shifts	136	117	86.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	233	206	88.4
¹³C chemical shifts	232	106	45.7
¹⁵N chemical shifts	113	96	85.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	483	442	91.5
¹³C chemical shifts	309	267	86.4
¹⁵N chemical shifts	23	21	91.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	67	97.1
¹³C chemical shifts	69	67	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	65	81.2
¹³C chemical shifts	75	46	61.3
¹⁵N chemical shifts	5	5	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 90.5%
- Total number of restraints: 3434
- Weight of restraints: 1.0 (3434)
- Potential type of restraints: square-well-parabolic (3434)
- Range of distance target values: 2.19, 4.35 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 44.8%
  - Total number of restraints: 62
  - Weight of restraints: 1.0 (62)
  - Potential type of restraints: square-well-parabolic (62)
  - Range of distance target values: 2.05, 2.62 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 80.2%
- Total number of restraints: 148
- Total number of restraints per polymer type: 148
- Weight of restraints: 1.0 (148)
- Potential type of restraints: square-well-parabolic (148)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), PSI-2, Protein NMR, Protein Structure Initiative, Structural Genomics, Target SgR46

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Found 1 Document (0.652 seconds)

BMRB: 16691

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. SgR46, : 1 : 1 : 25 entities Detail

Interaction partners 1. SgR46, : 5 interactors Detail

Experiments performed 24 experiments Detail

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