PDB-4j9a: Engineered Digoxigenin binder DIG10.3

ID or keywords:

Entry

Database: PDB / ID: 4j9a

Title

Engineered Digoxigenin binder DIG10.3

Components

Engineered Digoxigenin binder protein DIG10.3

Keywords

DIGOXIGENIN BINDING PROTEIN /

engineered / computationally designed / Digoxigenin-binding

Function / homology

SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta /

DIGOXIGENIN / Uncharacterized PhzA/B-like protein PA3332

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Stoddard, B.L. / Doyle, L.A.

Citation

Journal: Nature / Year: 2013
Title: Computational design of ligand-binding proteins with high affinity and selectivity.
Authors: Tinberg, C.E. / Khare, S.D. / Dou, J. / Doyle, L. / Nelson, J.W. / Schena, A. / Jankowski, W. / Kalodimos, C.G. / Johnsson, K. / Stoddard, B.L. / Baker, D.

History

Deposition	Feb 15, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 26, 2013	Provider: repository / Type: Initial release
Revision 1.1	Aug 14, 2013	Group: Database references
Revision 1.2	Sep 18, 2013	Group: Database references
Revision 1.3	Sep 25, 2013	Group: Database references
Revision 1.4	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.5	Feb 28, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4j9a.cif.gz	208.6 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j9/4j9a ftp://data.pdbj.org/pub/pdb/validation_reports/j9/4j9a	HTTPS FTP

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Related structure data

Related structure data	4j8tC C: citing same article (ref.)
Similar structure data	5gjh-2 4j6k-2 4wco-2 4j8t-4 2ogb-2 1mgw-d 3zgp-d 3qu6-3 1y9t-d 1o4b-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

4j8tC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: Engineered Digoxigenin binder protein DIG10.3

B: Engineered Digoxigenin binder protein DIG10.3

C: Engineered Digoxigenin binder protein DIG10.3

D: Engineered Digoxigenin binder protein DIG10.3

E: Engineered Digoxigenin binder protein DIG10.3

F: Engineered Digoxigenin binder protein DIG10.3

G: Engineered Digoxigenin binder protein DIG10.3

H: Engineered Digoxigenin binder protein DIG10.3

I: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

147 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by author
16.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by author
16.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by author
16.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by author
16.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by author
16.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by author
16.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by author
16.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

H: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by author
16.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

9

I: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by author
16.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

10

A: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

A: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by software
32.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

11

B: Engineered Digoxigenin binder protein DIG10.3

D: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by software
32.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

12

C: Engineered Digoxigenin binder protein DIG10.3

F: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by software
32.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

13

E: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

G: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by software
32.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

14

H: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

I: Engineered Digoxigenin binder protein DIG10.3

hetero molecules

defined by software
32.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	132.793, 90.993, 110.075
Angle α, β, γ (deg.)	90.000, 92.680, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASN	ASN	ARG	ARG	A	A	2 - 123	2 - 123
2	1	ASN	ASN	ARG	ARG	B	B	2 - 123	2 - 123
1	2	ASN	ASN	ARG	ARG	A	A	2 - 123	2 - 123
2	2	ASN	ASN	ARG	ARG	C	C	2 - 123	2 - 123
1	3	ASN	ASN	LEU	LEU	A	A	2 - 122	2 - 122
2	3	ASN	ASN	LEU	LEU	D	D	2 - 122	2 - 122
1	4	ASN	ASN	ARG	ARG	A	A	2 - 123	2 - 123
2	4	ASN	ASN	ARG	ARG	E	E	2 - 123	2 - 123
1	5	ASN	ASN	LEU	LEU	A	A	2 - 122	2 - 122
2	5	ASN	ASN	LEU	LEU	F	F	2 - 122	2 - 122
1	6	ASN	ASN	ARG	ARG	A	A	2 - 123	2 - 123
2	6	ASN	ASN	ARG	ARG	G	G	2 - 123	2 - 123
1	7	ASN	ASN	ARG	ARG	A	A	2 - 123	2 - 123
2	7	ASN	ASN	ARG	ARG	H	H	2 - 123	2 - 123
1	8	ASN	ASN	ARG	ARG	A	A	2 - 123	2 - 123
2	8	ASN	ASN	ARG	ARG	I	I	2 - 123	2 - 123
1	9	ASN	ASN	ARG	ARG	B	B	2 - 123	2 - 123
2	9	ASN	ASN	ARG	ARG	C	C	2 - 123	2 - 123
1	10	ASN	ASN	VAL	VAL	B	B	2 - 124	2 - 124
2	10	ASN	ASN	VAL	VAL	D	D	2 - 124	2 - 124
1	11	ASN	ASN	VAL	VAL	B	B	2 - 124	2 - 124
2	11	ASN	ASN	VAL	VAL	E	E	2 - 124	2 - 124
1	12	ASN	ASN	VAL	VAL	B	B	2 - 124	2 - 124
2	12	ASN	ASN	VAL	VAL	F	F	2 - 124	2 - 124
1	13	ASN	ASN	ARG	ARG	B	B	2 - 123	2 - 123
2	13	ASN	ASN	ARG	ARG	G	G	2 - 123	2 - 123
1	14	ASN	ASN	ARG	ARG	B	B	2 - 123	2 - 123
2	14	ASN	ASN	ARG	ARG	H	H	2 - 123	2 - 123
1	15	ASN	ASN	ARG	ARG	B	B	2 - 123	2 - 123
2	15	ASN	ASN	ARG	ARG	I	I	2 - 123	2 - 123
1	16	ASN	ASN	LEU	LEU	C	C	2 - 122	2 - 122
2	16	ASN	ASN	LEU	LEU	D	D	2 - 122	2 - 122
1	17	ASN	ASN	ARG	ARG	C	C	2 - 123	2 - 123
2	17	ASN	ASN	ARG	ARG	E	E	2 - 123	2 - 123
1	18	ASN	ASN	LEU	LEU	C	C	2 - 122	2 - 122
2	18	ASN	ASN	LEU	LEU	F	F	2 - 122	2 - 122
1	19	ASN	ASN	ARG	ARG	C	C	2 - 123	2 - 123
2	19	ASN	ASN	ARG	ARG	G	G	2 - 123	2 - 123
1	20	ASN	ASN	ARG	ARG	C	C	2 - 123	2 - 123
2	20	ASN	ASN	ARG	ARG	H	H	2 - 123	2 - 123
1	21	ASN	ASN	ARG	ARG	C	C	2 - 123	2 - 123
2	21	ASN	ASN	ARG	ARG	I	I	2 - 123	2 - 123
1	22	ASN	ASN	VAL	VAL	D	D	2 - 124	2 - 124
2	22	ASN	ASN	VAL	VAL	E	E	2 - 124	2 - 124
1	23	ASN	ASN	VAL	VAL	D	D	2 - 124	2 - 124
2	23	ASN	ASN	VAL	VAL	F	F	2 - 124	2 - 124
1	24	ASN	ASN	ARG	ARG	D	D	2 - 123	2 - 123
2	24	ASN	ASN	ARG	ARG	G	G	2 - 123	2 - 123
1	25	ASN	ASN	ARG	ARG	D	D	2 - 123	2 - 123
2	25	ASN	ASN	ARG	ARG	H	H	2 - 123	2 - 123
1	26	MET	MET	ARG	ARG	D	D	1 - 123	1 - 123
2	26	MET	MET	ARG	ARG	I	I	1 - 123	1 - 123
1	27	ASN	ASN	VAL	VAL	E	E	2 - 124	2 - 124
2	27	ASN	ASN	VAL	VAL	F	F	2 - 124	2 - 124
1	28	ASN	ASN	ARG	ARG	E	E	2 - 123	2 - 123
2	28	ASN	ASN	ARG	ARG	G	G	2 - 123	2 - 123
1	29	ASN	ASN	ARG	ARG	E	E	2 - 123	2 - 123
2	29	ASN	ASN	ARG	ARG	H	H	2 - 123	2 - 123
1	30	ASN	ASN	ARG	ARG	E	E	2 - 123	2 - 123
2	30	ASN	ASN	ARG	ARG	I	I	2 - 123	2 - 123
1	31	ASN	ASN	ARG	ARG	F	F	2 - 123	2 - 123
2	31	ASN	ASN	ARG	ARG	G	G	2 - 123	2 - 123
1	32	ASN	ASN	ARG	ARG	F	F	2 - 123	2 - 123
2	32	ASN	ASN	ARG	ARG	H	H	2 - 123	2 - 123
1	33	ASN	ASN	ARG	ARG	F	F	2 - 123	2 - 123
2	33	ASN	ASN	ARG	ARG	I	I	2 - 123	2 - 123
1	34	ASN	ASN	ARG	ARG	G	G	2 - 123	2 - 123
2	34	ASN	ASN	ARG	ARG	H	H	2 - 123	2 - 123
1	35	ASN	ASN	ARG	ARG	G	G	2 - 123	2 - 123
2	35	ASN	ASN	ARG	ARG	I	I	2 - 123	2 - 123
1	36	ASN	ASN	ARG	ARG	H	H	2 - 123	2 - 123
2	36	ASN	ASN	ARG	ARG	I	I	2 - 123	2 - 123

NCS ensembles :

#1: Protein	Engineered Digoxigenin binder protein DIG10.3 Mass: 15997.106 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Details: Computationally designed based on hypothetical protein PA3332 from Pseudomonas aeruginosa Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3332 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9HYR3
#2: Chemical	ChemComp-DOG / DIGOXIGENIN / 4-(3,12,14-TRIHYDROXY-10,13-DIMETHYL-HEXADECAHYDRO-CYCLOPENTA[A]PHENANTHREN-17-YL)-5H-FURAN-2-ONE / Digoxigenin Mass: 390.513 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂₃H₃₄O₅
Sequence details	DIG10.3 WAS COMPUTATIONALLY ENGINEERED BASED ON PRE-DEFINED CRITERIA OF AFFINITY FOR DIGOXIGENIN. ...DIG10.3 WAS COMPUTATIONALLY ENGINEERED BASED ON PRE-DEFINED CRITERIA OF AFFINITY FOR DIGOXIGENIN. THE FOLLOWING MUTATIONS TO PA3332 (PDB ID 1Z1S) WERE FOUND TO MAXIMIZE BINDING AND OPTIMIZE PROTEIN STABILITY: L7V, S10A, C23S, F34Y, A37P, W41Y, H61Y, L62M, V64I, A90L, V92A, Q99Y, S103A, L105W, D117L, W119F, H124V, A127P, G130L AND V131E. TO AIDE IN CRYSTALLIZATION THE C-TERMINAL RESIDUES 132-141 WERE REMOVED AND REPLACED WITH 6X HIS-TAG

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46.68 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2M Ammonium acetate, 0.1M Bis-Tris pH5.5, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.2 / Wavelength: 1.5998 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2012 / Details: mirrors

Radiation

Monochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5998 Å / Relative weight: 1

Reflection

Resolution: 3.2→50 Å / Num. obs: 21183 / % possible obs: 97.8 % / Redundancy: 7.3 % / R_merge(I) obs: 0.109 / Χ²: 1.066 / Net I/σ(I): 12.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
3.2-3.31	7.1	0.515	2082	1.023	1	96.5
3.31-3.45	7.2	0.351	2073	1.176	1	96.9
3.45-3.6	7.2	0.269	2097	1.173	1	97
3.6-3.79	7.3	0.221	2090	1.203	1	97.1
3.79-4.03	7.3	0.172	2104	1.141	1	97.7
4.03-4.34	7.4	0.125	2106	1.152	1	97.6
4.34-4.78	7.4	0.097	2136	1.015	1	98.2
4.78-5.47	7.3	0.088	2118	0.998	1	98.4
5.47-6.89	7	0.077	2165	0.941	1	98.9
6.89-50	7.3	0.059	2212	0.853	1	99.2

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.7.0029	refinement
PDB_EXTRACT	3.11	data extraction
BOS		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.2→45.54 Å / Cor.coef. F_o:F_c: 0.893 / Cor.coef. F_o:F_c free: 0.844 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.628 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3167	1082	5.1 %	RANDOM
R_work	0.2619	-	-	-
obs	0.2648	21172	97.49 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 153.95 Å² / B_iso mean: 72.708 Å² / B_iso min: 31.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.45 Å²	0 Å²	4.8 Å²
2-	-	9.2 Å²	0 Å²
3-	-	-	-5.95 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→45.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7045	0	252	0	7297

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	7585
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	5740
X-RAY DIFFRACTION	r_angle_refined_deg	1.736	1.969	10547
X-RAY DIFFRACTION	r_angle_other_deg	4.292	3	12982
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.179	5	1034
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.774	22.082	245
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.68	15	512
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.646	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	1152
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	9054
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	1869

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	4056	0.1
1	2	B	4056	0.1
2	1	A	3899	0.1
2	2	C	3899	0.1
3	1	A	3848	0.1
3	2	D	3848	0.1
4	1	A	3418	0.12
4	2	E	3418	0.12
5	1	A	3737	0.11
5	2	F	3737	0.11
6	1	A	2773	0.15
6	2	G	2773	0.15
7	1	A	3540	0.14
7	2	H	3540	0.14
8	1	A	3724	0.12
8	2	I	3724	0.12
9	1	B	3552	0.1
9	2	C	3552	0.1
10	1	B	3427	0.11
10	2	D	3427	0.11
11	1	B	3148	0.11
11	2	E	3148	0.11
12	1	B	3255	0.1
12	2	F	3255	0.1
13	1	B	2751	0.12
13	2	G	2751	0.12
14	1	B	3199	0.12
14	2	H	3199	0.12
15	1	B	3119	0.12
15	2	I	3119	0.12
16	1	C	3354	0.09
16	2	D	3354	0.09
17	1	C	3154	0.09
17	2	E	3154	0.09
18	1	C	3470	0.08
18	2	F	3470	0.08
19	1	C	2589	0.14
19	2	G	2589	0.14
20	1	C	3175	0.1
20	2	H	3175	0.1
21	1	C	3212	0.09
21	2	I	3212	0.09
22	1	D	2959	0.1
22	2	E	2959	0.1
23	1	D	3225	0.09
23	2	F	3225	0.09
24	1	D	2562	0.14
24	2	G	2562	0.14
25	1	D	3052	0.13
25	2	H	3052	0.13
26	1	D	3218	0.12
26	2	I	3218	0.12
27	1	E	2960	0.09
27	2	F	2960	0.09
28	1	E	2373	0.13
28	2	G	2373	0.13
29	1	E	2946	0.11
29	2	H	2946	0.11
30	1	E	2867	0.09
30	2	I	2867	0.09
31	1	F	2588	0.12
31	2	G	2588	0.12
32	1	F	2923	0.13
32	2	H	2923	0.13
33	1	F	3090	0.09
33	2	I	3090	0.09
34	1	G	2558	0.12
34	2	H	2558	0.12
35	1	G	2775	0.12
35	2	I	2775	0.12
36	1	H	3299	0.11
36	2	I	3299	0.11

LS refinement shell

Resolution: 3.204→3.287 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.4	78	-
R_work	0.297	1384	-
all	-	1462	-
obs	-	-	92.83 %

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About Yorodumi

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Yorodumi