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BMRB: 16744

2KUO

Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response

Authors

Li, G., McCulloch, R.D., Fenton, A., Cheung, M., Meng, L., Ikura, M., Koch, C.D.

Assembly

APLF

Entity

1. APLF Tandem ZF (polymer, Thiol state: all other bound), 91 monomers, 10255.18 Da Detail

GSKATDSVLQ GSEGNKVKRT SCMYGANCYR KNPVHFQHFS HPGDSDYGGV QIVGQDETDD RPECPYGPSC YRKNPQHKIE YRHNTLPVRN V

2. ZN (non-polymer, Thiol state: not present), 65.409 × 2 Da

Total weight

10385.998 Da

Max. entity weight

10255.18 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.8 %, Completeness (bb): 82.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.8 % (939 of 1034)	98.9 % (540 of 546)	78.1 % (307 of 393)	96.8 % (92 of 95)
Backbone	82.7 % (440 of 532)	98.4 % (181 of 184)	67.4 % (178 of 264)	96.4 % (81 of 84)
Sidechain	99.5 % (581 of 584)	99.2 % (359 of 362)	100.0 % (211 of 211)	100.0 % (11 of 11)
Aromatic	100.0 % (88 of 88)	100.0 % (44 of 44)	100.0 % (44 of 44)
Methyl	100.0 % (56 of 56)	100.0 % (28 of 28)	100.0 % (28 of 28)

1. APLF Tandem ZF

GSKATDSVLQ GSEGNKVKRT SCMYGANCYR KNPVHFQHFS HPGDSDYGGV QIVGQDETDD RPECPYGPSC YRKNPQHKIE YRHNTLPVRN V

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1), Details 13C,15N labeled APLF TZF(360-448)in H2O for 3D experimental data collection.

#	Name	Isotope labeling	Concentration
1	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	Bis-tris	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	1 mM
5	zinc chloride	natural abundance	0.05 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

Sample #2

Solvent system 99% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1), Details 13C,15N labeled APLF TZF(360-448)in D2O for 3D experimental data collection.

#	Name	Isotope labeling	Concentration
8	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
9	Bis-tris	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	1 mM
12	zinc chloride	natural abundance	0.05 mM
13	D2O	natural abundance	99 %

Sample #3

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1), Details 15N labeled APLF TZF(360-448)in H2O for NMR titrations.

#	Name	Isotope labeling	Concentration
14	APLF Tandem ZF	[U-100% 15N]	0.1 mM
15	Bis-tris	natural abundance	20 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	1 mM
18	zinc chloride	natural abundance	0.05 mM
19	H2O	natural abundance	93 %
20	D2O	natural abundance	7 %

Sample #4

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1), Details 15N labeled APLF TZF(360-448)in H2O for NMR titrations.

#	Name	Isotope labeling	Concentration
21	APLF Tandem ZF	[U-100% 15N]	0.1 mM
22	sodium phosphate	natural abundance	20 mM
23	potassium chloride	natural abundance	150 mM
24	sodium azide	natural abundance	1 mM
25	zinc chloride	natural abundance	0.05 mM
26	magnesium chloride	natural abundance	2 mM
27	H2O	natural abundance	93 %
28	D2O	natural abundance	7 %

Sample #5

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1), Details 15N labeled APLF TZF(360-448)in high salt H2O for RDC

#	Name	Isotope labeling	Concentration
29	APLF Tandem ZF	[U-100% 15N]	0.5 mM
30	Bis-tris	natural abundance	20 mM
31	sodium chloride	natural abundance	500 mM
32	sodium azide	natural abundance	1 mM
33	zinc chloride	natural abundance	0.05 mM
34	Pf1 phage	natural abundance	10 mg/mL
35	H2O	natural abundance	93 %
36	D2O	natural abundance	7 %

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: 0.06 ppm, Outliers: 5 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: 0.06 ppm, Outliers: 5 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: 2KUO, Strand ID: A Detail

Release date

2010-05-17

Citation

Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response
Li, G., McCulloch, R.D., Fenton, A.L., Cheung, M., Meng, L., Ikura, M., Koch, C.
Proc. Natl. Acad. Sci. U. S. A. (2010), 107, 9129-9134, PubMed 20439749 , DOI 10.1073/pnas.1000556107 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: Q8IW19 released on 2005-08-16
Title APLF_HUMAN Entity Aprataxin and PNK-like factor

Related entities 1. APLF Tandem ZF, : 1 : 4 : 30 entities Detail

Interaction partners 1. APLF Tandem ZF, : 9 interactors Detail

More details for 9 interactors identified by 5 citations

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1), Details 13C,15N labeled APLF TZF(360-448)in H2O for 3D experimental data collection.

#	Name	Isotope labeling	Concentration
1	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	Bis-tris	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	1 mM
5	zinc chloride	natural abundance	0.05 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 99% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1), Details 13C,15N labeled APLF TZF(360-448)in D2O for 3D experimental data collection.

#	Name	Isotope labeling	Concentration
8	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
9	Bis-tris	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	1 mM
12	zinc chloride	natural abundance	0.05 mM
13	D2O	natural abundance	99 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
9	Bis-tris	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	1 mM
12	zinc chloride	natural abundance	0.05 mM
13	D2O	natural abundance	99 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	Bis-tris	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	1 mM
5	zinc chloride	natural abundance	0.05 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

5 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	Bis-tris	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	1 mM
5	zinc chloride	natural abundance	0.05 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	Bis-tris	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	1 mM
5	zinc chloride	natural abundance	0.05 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

7 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	Bis-tris	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	1 mM
5	zinc chloride	natural abundance	0.05 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

8 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	Bis-tris	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	1 mM
5	zinc chloride	natural abundance	0.05 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
9	Bis-tris	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	1 mM
12	zinc chloride	natural abundance	0.05 mM
13	D2O	natural abundance	99 %

10 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	Bis-tris	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	1 mM
5	zinc chloride	natural abundance	0.05 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	Bis-tris	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	1 mM
5	zinc chloride	natural abundance	0.05 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

12 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	APLF Tandem ZF	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
9	Bis-tris	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	1 mM
12	zinc chloride	natural abundance	0.05 mM
13	D2O	natural abundance	99 %

13 2D 1H-15N IPAP HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1), Details 15N labeled APLF TZF(360-448)in high salt H2O for RDC

#	Name	Isotope labeling	Concentration
29	APLF Tandem ZF	[U-100% 15N]	0.5 mM
30	Bis-tris	natural abundance	20 mM
31	sodium chloride	natural abundance	500 mM
32	sodium azide	natural abundance	1 mM
33	zinc chloride	natural abundance	0.05 mM
34	Pf1 phage	natural abundance	10 mg/mL
35	H2O	natural abundance	93 %
36	D2O	natural abundance	7 %

14 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1), Details 15N labeled APLF TZF(360-448)in H2O for NMR titrations.

#	Name	Isotope labeling	Concentration
14	APLF Tandem ZF	[U-100% 15N]	0.1 mM
15	Bis-tris	natural abundance	20 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	1 mM
18	zinc chloride	natural abundance	0.05 mM
19	H2O	natural abundance	93 %
20	D2O	natural abundance	7 %

15 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.4 (±0.1), Details 15N labeled APLF TZF(360-448)in H2O for NMR titrations.

#	Name	Isotope labeling	Concentration
21	APLF Tandem ZF	[U-100% 15N]	0.1 mM
22	sodium phosphate	natural abundance	20 mM
23	potassium chloride	natural abundance	150 mM
24	sodium azide	natural abundance	1 mM
25	zinc chloride	natural abundance	0.05 mM
26	magnesium chloride	natural abundance	2 mM
27	H2O	natural abundance	93 %
28	D2O	natural abundance	7 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16744_2kuo.nef
Input source #2: Coordindates	2kuo.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:22:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:28:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:35:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:41:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:64:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:70:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:77:HIS:NE2	2:2:ZN:ZN	unknown	unknown	n/a
1:83:HIS:NE2	2:2:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None
B	2	ZN	ZINC ION	None

Sequence alignments

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

--360-----370-------380-------390-------400-------410-------420-------430-------440--------
GSKATDSVLQGSEGNKVKRTSCMYGANCYRKNPVHFQHFSHPGDSDYGGVQIVGQDETDDRPECPYGPSCYRKNPQHKIEYRHNTLPVRNV
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSKATDSVLQGSEGNKVKRTSCMYGANCYRKNPVHFQHFSHPGDSDYGGVQIVGQDETDDRPECPYGPSCYRKNPQHKIEYRHNTLPVRNV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	91	0	0	100.0

Content subtype: combined_16744_2kuo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	947		100.0 (chain: A, length: 91)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2718 (1)	noe	97.8 (chain: A, length: 91)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	18 (1)	hbond	17.6 (chain: A, length: 91)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	52 (52)	.	49.5 (chain: A, length: 91)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 550
  - ¹³C chemical shifts: 302
  - ¹⁵N chemical shifts: 95
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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)
376	ARG	HH21	6.672
376	ARG	HH22	6.672
418	ARG	HH11	7.157
418	ARG	HH12	7.157
418	ARG	HH21	6.403
418	ARG	HH22	6.403
439	ARG	HH11	6.804
439	ARG	HH12	6.804
439	ARG	HH21	6.718
439	ARG	HH22	6.718

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	546	540	98.9
¹³C chemical shifts	393	302	76.8
¹⁵N chemical shifts	101	95	94.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	184	181	98.4
¹³C chemical shifts	182	91	50.0
¹⁵N chemical shifts	84	81	96.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	362	359	99.2
¹³C chemical shifts	211	211	100.0
¹⁵N chemical shifts	17	14	82.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	29	100.0
¹³C chemical shifts	29	29	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	44	100.0
¹³C chemical shifts	44	44	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 97.8%
- Total number of restraints: 2718
- Weight of restraints: 1.0 (2718)
- Potential type of restraints: square-well-parabolic (2718)
- Range of distance target values: 2.25, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 17.6%
  - Total number of restraints: 18
  - Weight of restraints: 1.0 (18)
  - Potential type of restraints: square-well-parabolic (18)
  - Range of distance target values: 2.24, 3.29 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 49.5%
- Total number of restraints: 52
- Total number of restraints per polymer type: 52
- Weight of restraints: 1.0 (52)
- Potential type of restraints: square-well-parabolic (52)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords ADP-ribose, aprataxin PNK-like factor (APLF), DNA damage, PAR-binding zinc finger (PBZ), poly ADP-ribose (PAR)

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Found 1 Document (0.974 seconds)

BMRB: 16744

Sample #1

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. APLF Tandem ZF, : 1 : 4 : 30 entities Detail

Interaction partners 1. APLF Tandem ZF, : 9 interactors Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 5 contents Detail