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BMRB: 18545

2LUX

Calcium saturated form of human C85M S100A1 mutant

Authors

Ruszczynska-Bartnik, K., Budzinska, M., Zdanowski, K., Ejchart, A.

Assembly

C85M S100A1 dimer

Entity

1. S100A1C85M (polymer, Thiol state: not present), 93 monomers, 10442.54 × 2 Da Detail

GSELETAMET LINVFHAHSG KEGDKYKLSK KELKELLQTE LSGFLDAQKD VDAVDKVMKE LDENGDGEVD FQEYVVLVAA LTVAMNNFFW ENS

2. C85M S100A1 dimer, entity CA (non-polymer, Thiol state: not present), 40.078 × 4 Da

Total weight

21045.393 Da

Max. entity weight

10442.54 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation

Chem. Shift Complete

Sequence coverage: 98.9 %, Completeness: 90.7 %, Completeness (bb): 94.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.7 % (979 of 1079)	90.3 % (502 of 556)	90.7 % (382 of 421)	93.1 % (95 of 102)
Backbone	94.1 % (525 of 558)	93.2 % (179 of 192)	94.9 % (259 of 273)	93.5 % (87 of 93)
Sidechain	88.5 % (538 of 608)	88.7 % (323 of 364)	88.1 % (207 of 235)	88.9 % (8 of 9)
Aromatic	55.8 % (48 of 86)	55.8 % (24 of 43)	54.8 % (23 of 42)	100.0 % (1 of 1)
Methyl	97.2 % (103 of 106)	96.2 % (51 of 53)	98.1 % (52 of 53)

1. S100A1C85M

GSELETAMET LINVFHAHSG KEGDKYKLSK KELKELLQTE LSGFLDAQKD VDAVDKVMKE LDENGDGEVD FQEYVVLVAA LTVAMNNFFW ENS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	S100A1C85M	[U-98% 13C; U-98% 15N]	1 mM
2	TRIS	[U-99% 2H]	50 mM
3	sodium chloride	natural abundance	50 mM
4	CALCIUM ION	natural abundance	10 mM
5	D2O	[U-99% 2H]	10 %
6	H2O	natural abundance	90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
7	S100A1C85M	[U-98% 13C; U-98% 15N]	1 mM
8	TRIS	[U-99% 2H]	50 mM
9	sodium chloride	natural abundance	50 mM
10	CALCIUM ION	natural abundance	10 mM
11	D2O	[U-99% 2H]	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
12	S100A1C85M	[U-99% 15N]	1 mM
13	TRIS	[U-2H]	50 mM
14	sodium chloride	natural abundance	50 mM
15	CALCIUM ION	natural abundance	10 mM
16	D2O	[U-99% 2H]	10 %
17	H2O	natural abundance	90 %

LACS Plot; CA

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

Referencing offset: 0.12 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 0.12 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: 0.08 ppm, Outliers: 3 Detail

LACS Plot; CO

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

Referencing offset: -0.43 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Heteronucl. T₁

218 T₁ values in 3 lists
Coherence Sz, Field strength (¹H) 400 MHz, 500 MHz, 700 MHz, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1) Detail

Heteronucl. T₂

216 T₂ values in 3 lists
Coherence S(+,-), Field strength (¹H) 400 MHz, 500 MHz, 700 MHz, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1) Detail

Heteronucl. NOE

209 NOE values in 3 lists
Value type relative intensities, Field strength (¹H) 400 MHz, 500 MHz, 700 MHz, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1) Detail

Heteronucl. T₁/T₂

216 T₁/T₂ values in 3 lists
Field strength (¹H) 400 MHz, 500 MHz, 700 MHz, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1) Detail

Release date

2013-06-23

Citation

Solution structure of human holo-S100A1 C85M mutant
Ruszczynska-Bartnik, K., Ejchart, A., Budzinska, M., Zdanowski, K.
Not known

Related entities 1. S100A1C85M, : 1 : 1 : 9 : 257 entities Detail

Interaction partners 1. S100A1C85M, : 11 interactors Detail

More details for 11 interactors identified by 5 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	S100A1C85M	[U-98% 13C; U-98% 15N]	1 mM
2	TRIS	[U-99% 2H]	50 mM
3	sodium chloride	natural abundance	50 mM
4	CALCIUM ION	natural abundance	10 mM
5	D2O	[U-99% 2H]	10 %
6	H2O	natural abundance	90 %

2 2D 1H-13C HSQC aliphatic

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
7	S100A1C85M	[U-98% 13C; U-98% 15N]	1 mM
8	TRIS	[U-99% 2H]	50 mM
9	sodium chloride	natural abundance	50 mM
10	CALCIUM ION	natural abundance	10 mM
11	D2O	[U-99% 2H]	100 %

3 2D 1H-13C HSQC aromatic

Instrument

Varian Varian NMR System - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
7	S100A1C85M	[U-98% 13C; U-98% 15N]	1 mM
8	TRIS	[U-99% 2H]	50 mM
9	sodium chloride	natural abundance	50 mM
10	CALCIUM ION	natural abundance	10 mM
11	D2O	[U-99% 2H]	100 %

4 3D 1H-15N NOESY

Instrument

Varian Varian NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	S100A1C85M	[U-98% 13C; U-98% 15N]	1 mM
2	TRIS	[U-99% 2H]	50 mM
3	sodium chloride	natural abundance	50 mM
4	CALCIUM ION	natural abundance	10 mM
5	D2O	[U-99% 2H]	10 %
6	H2O	natural abundance	90 %

5 3D 1H-13C NOESY aliphatic

Instrument

Varian Varian NMR System - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
7	S100A1C85M	[U-98% 13C; U-98% 15N]	1 mM
8	TRIS	[U-99% 2H]	50 mM
9	sodium chloride	natural abundance	50 mM
10	CALCIUM ION	natural abundance	10 mM
11	D2O	[U-99% 2H]	100 %

6 3D 1H-13C NOESY aromatic

Instrument

Varian Varian NMR System - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
7	S100A1C85M	[U-98% 13C; U-98% 15N]	1 mM
8	TRIS	[U-99% 2H]	50 mM
9	sodium chloride	natural abundance	50 mM
10	CALCIUM ION	natural abundance	10 mM
11	D2O	[U-99% 2H]	100 %

7 3D CBCA(CO)NH

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	S100A1C85M	[U-98% 13C; U-98% 15N]	1 mM
2	TRIS	[U-99% 2H]	50 mM
3	sodium chloride	natural abundance	50 mM
4	CALCIUM ION	natural abundance	10 mM
5	D2O	[U-99% 2H]	10 %
6	H2O	natural abundance	90 %

8 3D HNCO

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	S100A1C85M	[U-98% 13C; U-98% 15N]	1 mM
2	TRIS	[U-99% 2H]	50 mM
3	sodium chloride	natural abundance	50 mM
4	CALCIUM ION	natural abundance	10 mM
5	D2O	[U-99% 2H]	10 %
6	H2O	natural abundance	90 %

9 3D HBHA(CO)NH

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	S100A1C85M	[U-98% 13C; U-98% 15N]	1 mM
2	TRIS	[U-99% 2H]	50 mM
3	sodium chloride	natural abundance	50 mM
4	CALCIUM ION	natural abundance	10 mM
5	D2O	[U-99% 2H]	10 %
6	H2O	natural abundance	90 %

10 3D HN(CO)CA

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	S100A1C85M	[U-98% 13C; U-98% 15N]	1 mM
2	TRIS	[U-99% 2H]	50 mM
3	sodium chloride	natural abundance	50 mM
4	CALCIUM ION	natural abundance	10 mM
5	D2O	[U-99% 2H]	10 %
6	H2O	natural abundance	90 %

11 1H-15N HSQC type NOE

Instrument

Varian INOVA - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
12	S100A1C85M	[U-99% 15N]	1 mM
13	TRIS	[U-2H]	50 mM
14	sodium chloride	natural abundance	50 mM
15	CALCIUM ION	natural abundance	10 mM
16	D2O	[U-99% 2H]	10 %
17	H2O	natural abundance	90 %

12 1H-15N HSQC type R1/R2

Instrument

Varian INOVA - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
12	S100A1C85M	[U-99% 15N]	1 mM
13	TRIS	[U-2H]	50 mM
14	sodium chloride	natural abundance	50 mM
15	CALCIUM ION	natural abundance	10 mM
16	D2O	[U-99% 2H]	10 %
17	H2O	natural abundance	90 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18545_2lux.nef
Input source #2: Coordindates	2lux.cif
Diamagnetism of the molecular assembly	False (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)
1:62:ASP:OD2	3:2:CA:CA	unknown	unknown	n/a
2:62:ASP:OD2	3:4:CA:CA	unknown	unknown	n/a
2:66:ASP:OD2	3:4:CA:CA	unknown	unknown	n/a
1:66:ASP:OD2	3:2:CA:CA	unknown	unknown	n/a
1:73:GLU:OE1	3:2:CA:CA	unknown	unknown	n/a
2:73:GLU:OE1	3:4:CA:CA	unknown	unknown	n/a
2:32:GLU:OE2	3:3:CA:CA	unknown	unknown	n/a
1:32:GLU:OE2	3:1:CA:CA	unknown	unknown	n/a
2:22:GLU:O	3:3:CA:CA	unknown	unknown	n/a
1:22:GLU:O	3:1:CA:CA	unknown	unknown	n/a
1:64:ASN:OD1	3:2:CA:CA	unknown	unknown	n/a
2:64:ASN:OD1	3:4:CA:CA	unknown	unknown	n/a
1:27:LYS:O	3:1:CA:CA	unknown	unknown	n/a
2:27:LYS:O	3:3:CA:CA	unknown	unknown	n/a
1:19:SER:O	3:1:CA:CA	unknown	unknown	n/a
2:19:SER:O	3:3:CA:CA	unknown	unknown	n/a
1:68:GLU:O	3:2:CA:CA	unknown	unknown	n/a
2:68:GLU:O	3:4:CA:CA	unknown	unknown	n/a
1:24:ASP:O	3:1:CA:CA	unknown	unknown	n/a
2:24:ASP:O	3:3:CA:CA	unknown	unknown	n/a
2:73:GLU:OE2	3:4:CA:CA	unknown	unknown	n/a
1:73:GLU:OE2	3:2:CA:CA	unknown	unknown	n/a
1:19:SER:OG	3:1:CA:CA	unknown	unknown	n/a
2:19:SER:OG	3:3:CA:CA	unknown	unknown	n/a
1:62:ASP:OD1	3:2:CA:CA	unknown	unknown	n/a
2:62:ASP:OD1	3:4:CA:CA	unknown	unknown	n/a
2:32:GLU:OE1	3:3:CA:CA	unknown	unknown	n/a
1:32:GLU:OE1	3:1:CA:CA	unknown	unknown	n/a
1:66:ASP:OD1	3:2:CA:CA	unknown	unknown	n/a
2:66:ASP:OD1	3:4:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	CA	CALCIUM ION	None
C	2	CA	CALCIUM ION	None
C	3	CA	CALCIUM ION	None
C	4	CA	CALCIUM ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90---
GSELETAMETLINVFHAHSGKEGDKYKLSKKELKELLQTELSGFLDAQKDVDAVDKVMKELDENGDGEVDFQEYVVLVAALTVAMNNFFWENS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSELETAMETLINVFHAHSGKEGDKYKLSKKELKELLQTELSGFLDAQKDVDAVDKVMKELDENGDGEVDFQEYVVLVAALTVAMNNFFWENS

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90---
GSELETAMETLINVFHAHSGKEGDKYKLSKKELKELLQTELSGFLDAQKDVDAVDKVMKELDENGDGEVDFQEYVVLVAALTVAMNNFFWENS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSELETAMETLINVFHAHSGKEGDKYKLSKKELKELLQTELSGFLDAQKDVDAVDKVMKELDENGDGEVDFQEYVVLVAALTVAMNNFFWENS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	93	0	0	100.0
B	B	93	0	0	100.0

Content subtype: combined_18545_2lux.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	30		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	995		98.9 (chain: A, length: 93)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	3838 (1)	noe	97.8 (chain: A, length: 93), 97.8 (chain: B, length: 93)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	140 (1)	hbond	58.1 (chain: A, length: 93), 58.1 (chain: B, length: 93)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	286 (286)	.	86.0 (chain: A, length: 93), 86.0 (chain: B, length: 93)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 98.9%
- Total number of assignments
  - ¹H chemical shifts: 516
  - ¹³C chemical shifts: 385
  - ¹⁵N chemical shifts: 94
- Completeness of assignments
  - Entity_assemble_ID: A
- 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)
90	TRP	CE2	137.815

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	556	516	92.8
¹³C chemical shifts	421	384	91.2
¹⁵N chemical shifts	102	94	92.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	192	184	95.8
¹³C chemical shifts	186	175	94.1
¹⁵N chemical shifts	93	86	92.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	364	332	91.2
¹³C chemical shifts	235	209	88.9
¹⁵N chemical shifts	9	8	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	56	100.0
¹³C chemical shifts	56	56	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	24	55.8
¹³C chemical shifts	42	23	54.8
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 97.8%
  - Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 97.8%
- Total number of restraints: 3818
- Weight of restraints: 1.0 (3818)
- Potential type of restraints: square-well-parabolic (3818)
- Range of distance target values: 2.55, 3.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 58.1%
    - Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 58.1%
  - Total number of restraints: 140
  - Weight of restraints: 1.0 (140)
  - Potential type of restraints: square-well-parabolic (140)
  - Range of distance target values: 1.85, 2.85 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
      None
  - 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: 93, Sequence coverage: 86.0%
  - Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 86.0%
- Total number of restraints: 286
- Total number of restraints per polymer type: 286
- Weight of restraints: 1.0 (286)
- Potential type of restraints: square-well-parabolic (286)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords 15N relaxation, C85MS100A1, C85M_S100A1 holo, C85M_S100A1 _holo, S100A1 C85M mutant

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Found 1 Document (1.155 seconds)

BMRB: 18545

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. S100A1C85M, : 1 : 1 : 9 : 257 entities Detail

Interaction partners 1. S100A1C85M, : 11 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 5 contents Detail