BMRBj - BMREntryMaster

Found 1 Document (1.212 seconds)

BMRB: 19394

2MBB

Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex

Authors

Wang, S., Zhou, P.

Assembly

human Polymerase iota UBM1-Ubiquitin Complex

Entity

1. GB1-UBM1 (polymer, Thiol state: all free), 106 monomers, 11977.07 Da Detail

MQYKLILNGK TLKGETTTEA VDAATAEKVF KQYANDNGVD GEWTYDDATK TFTVTEGSNE FPLCSLPEGV DQEVFKQLPV DIQEEILSGK SREKFQGKLE HHHHHH

2. ubiquitin (polymer, Thiol state: not present), 79 monomers, 8845.999 Da Detail

GSHMQIFVKT LTGKTITLEV EPSDTIENVK AKIQDKEGIP PDQQRLIFAG KQLEDGRTLS DYNIQKESTL HLVLRLRGG

Total weight

20823.07 Da

Max. entity weight

11977.07 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.7 %, Completeness: 84.7 %, Completeness (bb): 79.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.7 % (1835 of 2166)	92.3 % (1042 of 1129)	72.6 % (609 of 839)	92.9 % (184 of 198)
Backbone	79.2 % (870 of 1098)	92.1 % (349 of 379)	65.7 % (355 of 540)	92.7 % (166 of 179)
Sidechain	90.9 % (1125 of 1238)	92.4 % (693 of 750)	88.3 % (414 of 469)	94.7 % (18 of 19)
Aromatic	64.4 % (94 of 146)	80.8 % (59 of 73)	48.6 % (35 of 72)	0.0 % (0 of 1)
Methyl	99.5 % (201 of 202)	99.0 % (100 of 101)	100.0 % (101 of 101)

1. GB1-UBM1

MQYKLILNGK TLKGETTTEA VDAATAEKVF KQYANDNGVD GEWTYDDATK TFTVTEGSNE FPLCSLPEGV DQEVFKQLPV DIQEEILSGK SREKFQGKLE HHHHHH

2. ubiquitin

GSHMQIFVKT LTGKTITLEV EPSDTIENVK AKIQDKEGIP PDQQRLIFAG KQLEDGRTLS DYNIQKESTL HLVLRLRGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	GB1-UBM1	[U-100% 15N]	3 mM
2	ubiquitin	[U-100% 15N]	3 mM
3	potassium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	25 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
8	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
9	potassium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
13	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
14	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
15	potassium chloride	natural abundance	100 mM
16	sodium phosphate	natural abundance	25 mM
17	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
18	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
19	ubiquitin	natural abundance	3 mM
20	potassium chloride	natural abundance	100 mM
21	sodium phosphate	natural abundance	25 mM
22	D2O	natural abundance	100 %

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
23	GB1-UBM1	natural abundance	3 mM
24	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
25	potassium chloride	natural abundance	100 mM
26	sodium phosphate	natural abundance	25 mM
27	D2O	natural abundance	100 %

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: 0.51 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: 0.51 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: -0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2014-06-01

Citation

Sparsely-sampled, high-resolution 4-D omit spectra for detection and assignment of intermolecular NOEs of protein complexes
Wang, S., Zhou, P.
J. Biomol. NMR (2014), 59, 51-56, PubMed 24789524 , DOI 10.1007/s10858-014-9834-2 , Abstract

Related entities 1. GB1-UBM1, : 1 : 4 entities Detail

Related entities 2. ubiquitin, : 139 : 188 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	GB1-UBM1	[U-100% 15N]	3 mM
2	ubiquitin	[U-100% 15N]	3 mM
3	potassium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	25 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
13	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
14	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
15	potassium chloride	natural abundance	100 mM
16	sodium phosphate	natural abundance	25 mM
17	D2O	natural abundance	100 %

3 3D sparse-sampled HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
8	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
9	potassium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

4 3D sparse-sampled HNCA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
8	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
9	potassium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

5 3D sparse-sampled HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
8	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
9	potassium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

6 3D sparse-sampled HN(CO)CA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
8	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
9	potassium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	GB1-UBM1	[U-100% 15N]	3 mM
2	ubiquitin	[U-100% 15N]	3 mM
3	potassium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	25 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

8 3D sparse-sampled HN(COCA)CB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
8	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
9	potassium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

9 3D (HACA)CO(CA)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
8	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
9	potassium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

10 3D sparse-sampled HA(CACO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
8	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
9	potassium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

11 3D sparse-sampled HA(CA)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
8	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
9	potassium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

12 4D sparse-sampled HC(CO)NH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
8	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
9	potassium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

13 4D sparse-sampled CHNH NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
8	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
9	potassium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

14 4D sparse-sampled CHCH NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
13	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
14	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
15	potassium chloride	natural abundance	100 mM
16	sodium phosphate	natural abundance	25 mM
17	D2O	natural abundance	100 %

15 4D sparse-sampled CHCH NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
18	GB1-UBM1	[U-100% 13C; U-100% 15N]	3 mM
19	ubiquitin	natural abundance	3 mM
20	potassium chloride	natural abundance	100 mM
21	sodium phosphate	natural abundance	25 mM
22	D2O	natural abundance	100 %

16 4D sparse-sampled CHCH NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
23	GB1-UBM1	natural abundance	3 mM
24	ubiquitin	[U-100% 13C; U-100% 15N]	3 mM
25	potassium chloride	natural abundance	100 mM
26	sodium phosphate	natural abundance	25 mM
27	D2O	natural abundance	100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19394_2mbb.nef
Input source #2: Coordindates	2mbb.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
MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSNEFPLCSLPEGVDQEVFKQLPVDIQEEILSGKSREKFQGKLE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSNEFPLCSLPEGVDQEVFKQLPVDIQEEILSGKSREKFQGKLE

------
HHHHHH
||||||
HHHHHH

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

-200-----210-------220-------230-------240-------250-------260-------270------
SHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
--------10--------20--------30--------40--------50--------60--------70--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	106	0	0	100.0
B	B	78	0	0	100.0

Content subtype: combined_19394_2mbb.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1811		94.3 (chain: A, length: 106), 98.7 (chain: B, length: 78)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	6303 (1)	noe	35.8 (chain: A, length: 106), 97.4 (chain: B, length: 78)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	90 (1)	hbond	15.1 (chain: A, length: 106), 59.0 (chain: B, length: 78)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	190 (190)	.	35.8 (chain: A, length: 106), 94.9 (chain: B, length: 78)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 94.3%
  - Entity_assembly_ID: B, Chain length: 78, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 1045
  - ¹³C chemical shifts: 582
  - ¹⁵N chemical shifts: 184
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	638	571	89.5
¹³C chemical shifts	479	317	66.2
¹⁵N chemical shifts	115	105	91.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	217	200	92.2
¹³C chemical shifts	212	98	46.2
¹⁵N chemical shifts	103	95	92.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	421	371	88.1
¹³C chemical shifts	267	219	82.0
¹⁵N chemical shifts	12	10	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	53	100.0
¹³C chemical shifts	53	53	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	55	42	76.4
¹³C chemical shifts	54	24	44.4
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	488	474	97.1
¹³C chemical shifts	358	265	74.0
¹⁵N chemical shifts	87	79	90.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	159	155	97.5
¹³C chemical shifts	156	77	49.4
¹⁵N chemical shifts	75	71	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	329	319	97.0
¹³C chemical shifts	202	188	93.1
¹⁵N chemical shifts	12	8	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	50	100.0
¹³C chemical shifts	50	50	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	17	94.4
¹³C chemical shifts	18	11	61.1

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 35.8%
  - Entity_assembly_ID: B, Chain length: 78, Sequence coverage: 97.4%
- Total number of restraints: 6268
- Weight of restraints: 1.0 (6268)
- Potential type of restraints: upper-bound-parabolic (6268)
- Range of distance target values: 2.36, 7.3 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 15.1%
    - Entity_assembly_ID: B, Chain length: 78, Sequence coverage: 59.0%
  - Total number of restraints: 90
  - Weight of restraints: 1.0 (90)
  - Potential type of restraints: upper-bound-parabolic (90)
  - Range of distance target values: 2.5, 4.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 35.8%
  - Entity_assembly_ID: B, Chain length: 78, Sequence coverage: 94.9%
- Total number of restraints: 190
- Total number of restraints per polymer type: 190
- Weight of restraints: 1.0 (190)
- Potential type of restraints: square-well-parabolic (190)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: B

Keywords Polymerase iota, ubiquitin, UBM, UBM1

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Found 1 Document (1.212 seconds)

BMRB: 19394

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. GB1-UBM1, : 1 : 4 entities Detail

Related entities 2. ubiquitin, : 139 : 188 entities Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 5 contents Detail