PDB-1ok4: Archaeal fructose 1,6-bisphosphate aldolase covalently bound to t...

ID or keywords:

Entry

Database: PDB / ID: 1ok4

Title

Archaeal fructose 1,6-bisphosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate

Components

FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

Keywords

LYASE / ALDOLASE / FRUCTOSE 1 / 6-BISPHOSPHATE / TIM BARREL / GLYCOLYTIC / ARCHAEAL

Function / homology

Function and homology information

fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / cytoplasm
Similarity search - Function

Biological species

THERMOPROTEUS TENAX (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Lorentzen, E. / Zwart, P. / Stark, A. / Hensel, R. / Siebers, B. / Pohl, E.

Citation

Journal: J. Biol. Chem. / Year: 2003
Title: Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins.
Authors: Lorentzen, E. / Pohl, E. / Zwart, P. / Stark, A. / Russell, R.B. / Knura, T. / Hensel, R. / Siebers, B.

History

Deposition	Jul 17, 2003	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 4, 2003	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Mar 28, 2018	Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4	Jul 24, 2019	Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" "BA" "CA" IN EACH CHAIN ON SHEET ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1ok4.cif.gz	482.9 KB	Display	PDBx/mmCIF format
PDB format	pdb1ok4.ent.gz	398.5 KB	Display	PDB format
PDBx/mmJSON format	1ok4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1ok4_validation.pdf.gz	521.6 KB	Display	wwPDB validaton report
Full document	1ok4_full_validation.pdf.gz	547.1 KB	Display
Data in XML	1ok4_validation.xml.gz	90 KB	Display
Data in CIF	1ok4_validation.cif.gz	119.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ok/1ok4 ftp://data.pdbj.org/pub/pdb/validation_reports/ok/1ok4	HTTPS FTP

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Related structure data

Related structure data	1ojxSC 1ok6C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1ok6-1 1ok6-2 1w8s-2 2yce-2 1ojx-1 2yce-1 1w8s-1 1ojx-2 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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (7)

Deposited unit

A: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

B: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

C: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

D: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

E: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

F: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

G: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

H: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

I: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

J: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

hetero molecules

289 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

B: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

C: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

D: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

E: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

hetero molecules

defined by author&software
145 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

G: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

H: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

I: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

J: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I

hetero molecules

defined by author&software
145 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.400, 157.300, 101.500
Angle α, β, γ (deg.)	90.00, 108.20, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-ID	Component-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	ASP	ASP	A	A	3 - 24	3 - 24
2	1	ASN	ASN	ASP	ASP	B	B	3 - 24	3 - 24
3	1	ASN	ASN	ASP	ASP	C	C	3 - 24	3 - 24
4	1	ASN	ASN	ASP	ASP	D	D	3 - 24	3 - 24
5	1	ASN	ASN	ASP	ASP	E	E	3 - 24	3 - 24
6	1	ASN	ASN	ASP	ASP	F	F	3 - 24	3 - 24
7	1	ASN	ASN	ASP	ASP	G	G	3 - 24	3 - 24
8	1	ASN	ASN	ASP	ASP	H	H	3 - 24	3 - 24
9	1	ASN	ASN	ASP	ASP	I	I	3 - 24	3 - 24
10	1	ASN	ASN	ASP	ASP	J	J	3 - 24	3 - 24
1	2	GLY	GLY	PRO	PRO	A	A	30 - 43	30 - 43
2	2	GLY	GLY	PRO	PRO	B	B	30 - 43	30 - 43
3	2	GLY	GLY	PRO	PRO	C	C	30 - 43	30 - 43
4	2	GLY	GLY	PRO	PRO	D	D	30 - 43	30 - 43
5	2	GLY	GLY	PRO	PRO	E	E	30 - 43	30 - 43
6	2	GLY	GLY	PRO	PRO	F	F	30 - 43	30 - 43
7	2	GLY	GLY	PRO	PRO	G	G	30 - 43	30 - 43
8	2	GLY	GLY	PRO	PRO	H	H	30 - 43	30 - 43
9	2	GLY	GLY	PRO	PRO	I	I	30 - 43	30 - 43
10	2	GLY	GLY	PRO	PRO	J	J	30 - 43	30 - 43
1	3	ASP	ASP	TYR	TYR	A	A	52 - 86	52 - 86
2	3	ASP	ASP	TYR	TYR	B	B	52 - 86	52 - 86
3	3	ASP	ASP	TYR	TYR	C	C	52 - 86	52 - 86
4	3	ASP	ASP	TYR	TYR	D	D	52 - 86	52 - 86
5	3	ASP	ASP	TYR	TYR	E	E	52 - 86	52 - 86
6	3	ASP	ASP	TYR	TYR	F	F	52 - 86	52 - 86
7	3	ASP	ASP	TYR	TYR	G	G	52 - 86	52 - 86
8	3	ASP	ASP	TYR	TYR	H	H	52 - 86	52 - 86
9	3	ASP	ASP	TYR	TYR	I	I	52 - 86	52 - 86
10	3	ASP	ASP	TYR	TYR	J	J	52 - 86	52 - 86
1	4	GLY	GLY	LYS	LYS	A	A	88 - 131	88 - 131
2	4	GLY	GLY	LYS	LYS	B	B	88 - 131	88 - 131
3	4	GLY	GLY	LYS	LYS	C	C	88 - 131	88 - 131
4	4	GLY	GLY	LYS	LYS	D	D	88 - 131	88 - 131
5	4	GLY	GLY	LYS	LYS	E	E	88 - 131	88 - 131
6	4	GLY	GLY	LYS	LYS	F	F	88 - 131	88 - 131
7	4	GLY	GLY	LYS	LYS	G	G	88 - 131	88 - 131
8	4	GLY	GLY	LYS	LYS	H	H	88 - 131	88 - 131
9	4	GLY	GLY	LYS	LYS	I	I	88 - 131	88 - 131
10	4	GLY	GLY	LYS	LYS	J	J	88 - 131	88 - 131
1	5	ASP	ASP	LYS	LYS	A	A	133 - 151	133 - 151
2	5	ASP	ASP	LYS	LYS	B	B	133 - 151	133 - 151
3	5	ASP	ASP	LYS	LYS	C	C	133 - 151	133 - 151
4	5	ASP	ASP	LYS	LYS	D	D	133 - 151	133 - 151
5	5	ASP	ASP	LYS	LYS	E	E	133 - 151	133 - 151
6	5	ASP	ASP	LYS	LYS	F	F	133 - 151	133 - 151
7	5	ASP	ASP	LYS	LYS	G	G	133 - 151	133 - 151
8	5	ASP	ASP	LYS	LYS	H	H	133 - 151	133 - 151
9	5	ASP	ASP	LYS	LYS	I	I	133 - 151	133 - 151
10	5	ASP	ASP	LYS	LYS	J	J	133 - 151	133 - 151
1	6	THR	THR	GLU	GLU	A	A	156 - 210	156 - 210
2	6	THR	THR	GLU	GLU	B	B	156 - 210	156 - 210
3	6	THR	THR	GLU	GLU	C	C	156 - 210	156 - 210
4	6	THR	THR	GLU	GLU	D	D	156 - 210	156 - 210
5	6	THR	THR	GLU	GLU	E	E	156 - 210	156 - 210
6	6	THR	THR	GLU	GLU	F	F	156 - 210	156 - 210
7	6	THR	THR	GLU	GLU	G	G	156 - 210	156 - 210
8	6	THR	THR	GLU	GLU	H	H	156 - 210	156 - 210
9	6	THR	THR	GLU	GLU	I	I	156 - 210	156 - 210
10	6	THR	THR	GLU	GLU	J	J	156 - 210	156 - 210
1	7	ALA	ALA	ARG	ARG	A	A	223 - 237	223 - 237
2	7	ALA	ALA	ARG	ARG	B	B	223 - 237	223 - 237
3	7	ALA	ALA	ARG	ARG	C	C	223 - 237	223 - 237
4	7	ALA	ALA	ARG	ARG	D	D	223 - 237	223 - 237
5	7	ALA	ALA	ARG	ARG	E	E	223 - 237	223 - 237
6	7	ALA	ALA	ARG	ARG	F	F	223 - 237	223 - 237
7	7	ALA	ALA	ARG	ARG	G	G	223 - 237	223 - 237
8	7	ALA	ALA	ARG	ARG	H	H	223 - 237	223 - 237
9	7	ALA	ALA	ARG	ARG	I	I	223 - 237	223 - 237
10	7	ALA	ALA	ARG	ARG	J	J	223 - 237	223 - 237
1	8	ASP	ASP	VAL	VAL	A	A	239 - 251	239 - 251
2	8	ASP	ASP	VAL	VAL	B	B	239 - 251	239 - 251
3	8	ASP	ASP	VAL	VAL	C	C	239 - 251	239 - 251
4	8	ASP	ASP	VAL	VAL	D	D	239 - 251	239 - 251
5	8	ASP	ASP	VAL	VAL	E	E	239 - 251	239 - 251
6	8	ASP	ASP	VAL	VAL	F	F	239 - 251	239 - 251
7	8	ASP	ASP	VAL	VAL	G	G	239 - 251	239 - 251
8	8	ASP	ASP	VAL	VAL	H	H	239 - 251	239 - 251
9	8	ASP	ASP	VAL	VAL	I	I	239 - 251	239 - 251
10	8	ASP	ASP	VAL	VAL	J	J	239 - 251	239 - 251

NCS oper: (Code: given
Matrix: (0.96895, -0.16745, -0.18194), (-0.11733, 0.33637, -0.93439), (0.21767, 0.92672, 0.30628)
Vector: 21.34281, 90.45076, -70.82803)

#1: Protein	FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I / FBP ALDOLASE Mass: 28741.064 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Details: LYS177 SCHIFF-BASE WITH DHAP / Source: (gene. exp.) THERMOPROTEUS TENAX (archaea) / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P58315, fructose-bisphosphate aldolase
#2: Chemical	ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE Mass: 170.058 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₇O₆P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H₂O
Compound details	LYSINE 177 FORMS A SCHIFF-BASE WITH DIHYDROXYACETONE PHOSPHATE SUBSTRATE. ASP 24 IS THE GENERAL ...LYSINE 177 FORMS A SCHIFF-BASE WITH DIHYDROXYACETONE PHOSPHATE SUBSTRATE. ASP 24 IS THE GENERAL BASE, TYR 146 IS THE PROTON DONOR.

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Experiment

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

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Sample preparation

Crystal

Density Matthews: 2.3 Å³/Da / Density % sol: 45 %

Crystal grow

pH: 5
Details: 9% (W/V) PEG 4000, 0.1 M NA ACETATE PH 5.0, 1-8% GLYCEROL, 100 MM DHAP

Crystal grow

*PLUS

Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details	Chemical formula
1	3 mg/ml	protein	1	drop
2	10 mM	HEPES-NaOH	1	drop	pH7.5
3	100 mM		1	drop		KCl
4	1 mM	dithiothreitol	1	drop
5	9 %(w/v)	PEG4000	1	reservoir
6	0.1 M	sodium acetate	1	reservoir	pH5.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.845
Detector	Date: Feb 15, 2002
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.845 Å / Relative weight: 1
Reflection	Resolution: 2.1→40 Å / Num. obs: 125363 / % possible obs: 90.2 % / Redundancy: 3.6 % / R_merge(I) obs: 0.071 / Net I/σ(I): 13.6
Reflection shell	Resolution: 2.1→2.19 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.272 / Mean I/σ(I) obs: 2.3 / % possible all: 59.3
Reflection	PLUS Highest resolution: 2.1 Å / Lowest resolution: 40 Å / R_merge(I) obs*: 0.071
Reflection shell	PLUS % possible obs: 59.3 % / R_merge(I) obs: 0.272 / Mean I/σ(I) obs*: 2.3

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Processing

Software

Name	Version	Classification
REFMAC	5.1.19	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OJX

1ojx

Resolution: 2.1→36.51 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.952 / SU B: 4.797 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.185	3203	2.5 %	RANDOM
R_work	0.163	-	-	-
obs	0.164	125363	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 10.04 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.07 Å²	0 Å²	0.07 Å²
2-	-	-0.12 Å²	0 Å²
3-	-	-	0.24 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→36.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19358	0	90	641	20089

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	19878
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	18456
X-RAY DIFFRACTION	r_angle_refined_deg	1.275	1.97	26890
X-RAY DIFFRACTION	r_angle_other_deg	0.834	3	42784
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.666	5	2492
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	2930
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	22114
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	4162
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	3982
X-RAY DIFFRACTION	r_nbd_other	0.239	0.2	20513
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	10681
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	802
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.327	0.2	23
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.37	0.2	64
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.255	0.2	12
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.603	1.5	12378
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.295	2	19780
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.199	3	7500
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.916	4.5	7110
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 3226 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.03	0.05
2	B	tight positional	0.03	0.05
3	C	tight positional	0.02	0.05
4	D	tight positional	0.02	0.05
5	E	tight positional	0.03	0.05
6	F	tight positional	0.02	0.05
7	G	tight positional	0.03	0.05
8	H	tight positional	0.03	0.05
9	I	tight positional	0.02	0.05
10	J	tight positional	0.03	0.05
1	A	tight thermal	0.09	0.5
2	B	tight thermal	0.11	0.5
3	C	tight thermal	0.09	0.5
4	D	tight thermal	0.08	0.5
5	E	tight thermal	0.1	0.5
6	F	tight thermal	0.09	0.5
7	G	tight thermal	0.1	0.5
8	H	tight thermal	0.1	0.5
9	I	tight thermal	0.09	0.5
10	J	tight thermal	0.1	0.5

LS refinement shell

Resolution: 2.1→2.15 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.26	158
R_work	0.249	5639

Refinement

*PLUS

Lowest resolution: 40 Å / R_factor R_free: 0.187 / R_factor R_work: 0.16

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.013
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.3

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