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BMRB: 19472

2MD7

1H, 13C, and 15N Chemical Shift Assignments for Sp140 PHD finger trans conformer

Authors

Zucchelli, C., Quilici, G., Musco, G.

Assembly

Sp140 PHD finger trans conformer

Entity

1. Sp140 PHD finger trans conformer (polymer, Thiol state: disulfide and other bound), 56 monomers, 6428.298 Da Detail

GAMGMRNLDE CEVCRDGGEL FCCDTCSRVF HEDCHIPPVE AERTPWNCIF CRMKES

2. ZINC ION (non-polymer), 65.409 × 2 Da

Total weight

6559.1157 Da

Max. entity weight

6428.298 Da

Entity Connection

disulfide 1, metal coordination 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:CYS11:SG	2:ZN1:ZN
2	metal coordination	sing	1:CYS14:SG	2:ZN1:ZN
3	metal coordination	sing	1:HIS31:NE2	2:ZN1:ZN
4	metal coordination	sing	1:HIS35:NE2	2:ZN1:ZN
5	disulfide	sing	1:CYS22:SG	1:CYS34:SG
6	metal coordination	sing	1:CYS23:SG	2:ZN1:ZN
7	metal coordination	sing	1:CYS26:SG	2:ZN1:ZN
8	metal coordination	sing	1:CYS48:SG	2:ZN1:ZN
9	metal coordination	sing	1:CYS51:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing, distance geometry

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 83.1 %, Completeness (bb): 96.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.1 % (516 of 621)	94.2 % (306 of 325)	65.4 % (157 of 240)	94.6 % (53 of 56)
Backbone	96.4 % (318 of 330)	96.5 % (109 of 113)	95.1 % (156 of 164)	100.0 % (53 of 53)
Sidechain	72.6 % (249 of 343)	92.9 % (197 of 212)	40.6 % (52 of 128)	0.0 % (0 of 3)
Aromatic	50.0 % (25 of 50)	100.0 % (25 of 25)	0.0 % (0 of 24)	0.0 % (0 of 1)
Methyl	58.3 % (21 of 36)	100.0 % (18 of 18)	16.7 % (3 of 18)

1. Sp140 PHD finger trans conformer

GAMGMRNLDE CEVCRDGGEL FCCDTCSRVF HEDCHIPPVE AERTPWNCIF CRMKES

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	Sp140 PHD finger	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate buffer pH 6.3	natural abundance	20 mM
3	NaCl	natural abundance	150 mM
4	DTT	natural abundance	4 mM
5	ZnCl2	natural abundance	50 uM
6	DSS	natural abundance	0.3 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
9	Sp140 PHD finger	[U-100% 13C; U-100% 15N]	1 mM
10	sodium phosphate buffer pH 6.3	natural abundance	20 mM
11	NaCl	natural abundance	150 mM
12	DTT	natural abundance	4 mM
13	ZnCl2	natural abundance	50 uM
14	DSS	natural abundance	0.3 mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
17	Sp140 PHD finger	[U-100% 15N]	1 mM
18	sodium phosphate buffer pH 6.3	natural abundance	20 mM
19	NaCl	natural abundance	150 mM
20	DTT	natural abundance	4 mM
21	ZnCl2	natural abundance	50 uM
22	DSS	natural abundance	0.3 mM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

Sample #4

Solvent system 100% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
25	Sp140 PHD finger	natural abundance	1 mM
26	sodium phosphate buffer pH 6.3	natural abundance	20 mM
27	NaCl	natural abundance	150 mM
28	DTT	natural abundance	4 mM
29	ZnCl2	natural abundance	50 uM
30	DSS	natural abundance	0.3 mM
31	H2O	natural abundance	90 %
32	D2O	natural abundance	10 %

Sample #5

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
33	Sp140 PHD finger	natural abundance	1 mM
34	sodium phosphate buffer pH 6.3	natural abundance	20 mM
35	NaCl	natural abundance	150 mM
36	DTT	natural abundance	4 mM
37	ZnCl2	natural abundance	50 uM
38	DSS	natural abundance	0.3 mM
39	H2O	natural abundance	90 %
40	D2O	natural abundance	10 %

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: -0.15 ppm, Outliers: 2 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: -0.15 ppm, Outliers: 2 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

LACS Plot; CO

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: -0.08 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MD7, Strand ID: B Detail

Release date

2013-09-18

Citation

Structure of human Sp140 PHD finger: an atypical fold interacting with Pin1
Zucchelli, C., Tamburri, S., Quilici, G., Palagano, E., Berardi, A., Saare, M., Peterson, P., Bachi, A., Musco, G.
FEBS J. (2014), 281, 216-231, PubMed 24267382 , DOI 10.1111/febs.12588 , Abstract

Related entities 1. Sp140 PHD finger trans conformer, : 1 : 1 : 3 : 226 entities Detail

Interaction partners 1. Sp140 PHD finger trans conformer, : 3 interactors Detail

More details for 3 interactors identified by 2 citations

Experiments performed 17 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	Sp140 PHD finger	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate buffer pH 6.3	natural abundance	20 mM
3	NaCl	natural abundance	150 mM
4	DTT	natural abundance	4 mM
5	ZnCl2	natural abundance	50 uM
6	DSS	natural abundance	0.3 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	Sp140 PHD finger	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate buffer pH 6.3	natural abundance	20 mM
3	NaCl	natural abundance	150 mM
4	DTT	natural abundance	4 mM
5	ZnCl2	natural abundance	50 uM
6	DSS	natural abundance	0.3 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
25	Sp140 PHD finger	natural abundance	1 mM
26	sodium phosphate buffer pH 6.3	natural abundance	20 mM
27	NaCl	natural abundance	150 mM
28	DTT	natural abundance	4 mM
29	ZnCl2	natural abundance	50 uM
30	DSS	natural abundance	0.3 mM
31	H2O	natural abundance	90 %
32	D2O	natural abundance	10 %

4 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
33	Sp140 PHD finger	natural abundance	1 mM
34	sodium phosphate buffer pH 6.3	natural abundance	20 mM
35	NaCl	natural abundance	150 mM
36	DTT	natural abundance	4 mM
37	ZnCl2	natural abundance	50 uM
38	DSS	natural abundance	0.3 mM
39	H2O	natural abundance	90 %
40	D2O	natural abundance	10 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
25	Sp140 PHD finger	natural abundance	1 mM
26	sodium phosphate buffer pH 6.3	natural abundance	20 mM
27	NaCl	natural abundance	150 mM
28	DTT	natural abundance	4 mM
29	ZnCl2	natural abundance	50 uM
30	DSS	natural abundance	0.3 mM
31	H2O	natural abundance	90 %
32	D2O	natural abundance	10 %

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
33	Sp140 PHD finger	natural abundance	1 mM
34	sodium phosphate buffer pH 6.3	natural abundance	20 mM
35	NaCl	natural abundance	150 mM
36	DTT	natural abundance	4 mM
37	ZnCl2	natural abundance	50 uM
38	DSS	natural abundance	0.3 mM
39	H2O	natural abundance	90 %
40	D2O	natural abundance	10 %

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	Sp140 PHD finger	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate buffer pH 6.3	natural abundance	20 mM
3	NaCl	natural abundance	150 mM
4	DTT	natural abundance	4 mM
5	ZnCl2	natural abundance	50 uM
6	DSS	natural abundance	0.3 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

8 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	Sp140 PHD finger	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate buffer pH 6.3	natural abundance	20 mM
3	NaCl	natural abundance	150 mM
4	DTT	natural abundance	4 mM
5	ZnCl2	natural abundance	50 uM
6	DSS	natural abundance	0.3 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

9 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	Sp140 PHD finger	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate buffer pH 6.3	natural abundance	20 mM
3	NaCl	natural abundance	150 mM
4	DTT	natural abundance	4 mM
5	ZnCl2	natural abundance	50 uM
6	DSS	natural abundance	0.3 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

10 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	Sp140 PHD finger	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate buffer pH 6.3	natural abundance	20 mM
3	NaCl	natural abundance	150 mM
4	DTT	natural abundance	4 mM
5	ZnCl2	natural abundance	50 uM
6	DSS	natural abundance	0.3 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

11 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	Sp140 PHD finger	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate buffer pH 6.3	natural abundance	20 mM
3	NaCl	natural abundance	150 mM
4	DTT	natural abundance	4 mM
5	ZnCl2	natural abundance	50 uM
6	DSS	natural abundance	0.3 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

12 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
17	Sp140 PHD finger	[U-100% 15N]	1 mM
18	sodium phosphate buffer pH 6.3	natural abundance	20 mM
19	NaCl	natural abundance	150 mM
20	DTT	natural abundance	4 mM
21	ZnCl2	natural abundance	50 uM
22	DSS	natural abundance	0.3 mM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

13 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	Sp140 PHD finger	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate buffer pH 6.3	natural abundance	20 mM
3	NaCl	natural abundance	150 mM
4	DTT	natural abundance	4 mM
5	ZnCl2	natural abundance	50 uM
6	DSS	natural abundance	0.3 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

14 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
9	Sp140 PHD finger	[U-100% 13C; U-100% 15N]	1 mM
10	sodium phosphate buffer pH 6.3	natural abundance	20 mM
11	NaCl	natural abundance	150 mM
12	DTT	natural abundance	4 mM
13	ZnCl2	natural abundance	50 uM
14	DSS	natural abundance	0.3 mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

15 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
17	Sp140 PHD finger	[U-100% 15N]	1 mM
18	sodium phosphate buffer pH 6.3	natural abundance	20 mM
19	NaCl	natural abundance	150 mM
20	DTT	natural abundance	4 mM
21	ZnCl2	natural abundance	50 uM
22	DSS	natural abundance	0.3 mM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

16 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
9	Sp140 PHD finger	[U-100% 13C; U-100% 15N]	1 mM
10	sodium phosphate buffer pH 6.3	natural abundance	20 mM
11	NaCl	natural abundance	150 mM
12	DTT	natural abundance	4 mM
13	ZnCl2	natural abundance	50 uM
14	DSS	natural abundance	0.3 mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

17 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
9	Sp140 PHD finger	[U-100% 13C; U-100% 15N]	1 mM
10	sodium phosphate buffer pH 6.3	natural abundance	20 mM
11	NaCl	natural abundance	150 mM
12	DTT	natural abundance	4 mM
13	ZnCl2	natural abundance	50 uM
14	DSS	natural abundance	0.3 mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19472_2md7.nef
Input source #2: Coordindates	2md7.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
B:22:CYS:SG	B:34:CYS:SG	oxidized, CA 52.441, CB 50.915 ppm	oxidized, CA 59.183, CB 42.809 ppm	2.026

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)
1:35:HIS:NE2	2:2:ZN:ZN	unknown	unknown	n/a
1:31:HIS:NE2	2:2:ZN:ZN	unknown	unknown	n/a
1:26:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:14:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:11:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:51:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:23:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:48:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

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

Sequence alignments

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
B	B	56	0	0	100.0

Content subtype: combined_19472_2md7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	9		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	524		100.0 (chain: B, length: 56)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	1091 (1)	noe	100.0 (chain: B, length: 56)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 56, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 313
  - ¹³C chemical shifts: 159
  - ¹⁵N chemical shifts: 52
- Completeness of assignments
  - Entity_assemble_ID: B
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
31	HIS	HD1	11.623
35	HIS	HD1	11.401

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	325	311	95.7
¹³C chemical shifts	240	159	66.2
¹⁵N chemical shifts	61	52	85.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	113	111	98.2
¹³C chemical shifts	112	107	95.5
¹⁵N chemical shifts	53	52	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	212	200	94.3
¹³C chemical shifts	128	52	40.6
¹⁵N chemical shifts	8	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	18	85.7
¹³C chemical shifts	21	2	9.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	25	100.0
¹³C chemical shifts	24	0	0.0
¹⁵N chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 56, Sequence coverage: 100.0%
- Total number of restraints: 1091
- Weight of restraints: 1.0 (1091)
- Potential type of restraints: square-well-parabolic (1091)
- Range of distance target values: 1.68, 6.13 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
- Distance restraints on contact map

Keywords PHD finger, Sp140

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Found 1 Document (0.674 seconds)

BMRB: 19472

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Sp140 PHD finger trans conformer, : 1 : 1 : 3 : 226 entities Detail

Interaction partners 1. Sp140 PHD finger trans conformer, : 3 interactors Detail

Experiments performed 17 experiments Detail

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NMR combined restraints 3 contents Detail