PDB-3aq0: Ligand-bound form of Arabidopsis medium/long-chain length prenyl ...

ID or keywords:

Entry

Database: PDB / ID: 3aq0

Title

Ligand-bound form of Arabidopsis medium/long-chain length prenyl pyrophosphate synthase (surface polar residue mutant)

Components

Geranyl diphosphate synthase

Keywords

TRANSFERASE / prenyltransferase / All alpha-helices fold / chroloplast / isoprenoid biosynthetic process

Function / homology

Function and homology information

all-trans-nonaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific] / all-trans-nonaprenyl-diphosphate synthase (geranylgeranyl-diphosphate specific) activity / embryo development ending in seed dormancy / prenyltransferase activity / ubiquinone biosynthetic process / isoprenoid biosynthetic process / plastid / chloroplast / mitochondrion / metal ion binding
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.65 Å

Authors

Hsieh, F.-L. / Chang, T.-H. / Ko, T.-P. / Wang, A.H.-J.

Citation

Journal: Plant Physiol. / Year: 2011
Title: Structure and mechanism of an Arabidopsis medium/long-chain-length prenyl pyrophosphate synthase
Authors: Hsieh, F.-L. / Chang, T.-H. / Ko, T.-P. / Wang, A.H.-J.

History

Deposition	Oct 24, 2010	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 19, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jan 29, 2014	Group: Database references
Revision 1.3	Oct 11, 2017	Group: Refinement description / Category: software
Revision 1.4	Nov 1, 2023	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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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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Download

PDBx/mmCIF format	3aq0.cif.gz	996.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3aq0_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	3aq0_full_validation.pdf.gz	2.4 MB	Display
Data in XML	3aq0_validation.xml.gz	108.5 KB	Display
Data in CIF	3aq0_validation.cif.gz	141.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aq/3aq0 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/3aq0	HTTPS FTP

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Related structure data

Related structure data	3apzSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2f7f-1 2zze-1 2zzg-1 3ffk-2 3bdn-d 4qp2-d 2zzf-d 6pnc-d 3qnf-3 2zzg-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) 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

Related structure data

3apzSC

S: Starting model for refinement

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	#201 - Sep 2016 Isoprene Synthase similarity (6)

Deposited unit

A: Geranyl diphosphate synthase

B: Geranyl diphosphate synthase

C: Geranyl diphosphate synthase

D: Geranyl diphosphate synthase

E: Geranyl diphosphate synthase

F: Geranyl diphosphate synthase

G: Geranyl diphosphate synthase

H: Geranyl diphosphate synthase

hetero molecules

307 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Geranyl diphosphate synthase

B: Geranyl diphosphate synthase

hetero molecules

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

2

C: Geranyl diphosphate synthase

D: Geranyl diphosphate synthase

hetero molecules

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

3

E: Geranyl diphosphate synthase

F: Geranyl diphosphate synthase

hetero molecules

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

4

G: Geranyl diphosphate synthase

H: Geranyl diphosphate synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	115.961, 115.961, 385.874
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	H
1	2	E
2	2	C
1	3	B
2	3	G
1	4	D
2	4	F

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	PRO	LYS	LYS	4	A	A	10 - 35	10 - 35
2	1	1	PRO	PRO	LYS	LYS	4	H	H	10 - 35	10 - 35
1	2	1	LEU	LEU	LEU	LEU	3	A	A	36 - 65	36 - 65
2	2	1	LEU	LEU	LEU	LEU	3	H	H	36 - 65	36 - 65
1	3	1	VAL	VAL	HIS	HIS	2	A	A	87 - 106	87 - 106
2	3	1	VAL	VAL	HIS	HIS	2	H	H	87 - 106	87 - 106
1	4	1	ASP	ASP	GLY	GLY	4	A	A	107 - 120	107 - 120
2	4	1	ASP	ASP	GLY	GLY	4	H	H	107 - 120	107 - 120
1	5	1	SER	SER	THR	THR	2	A	A	121 - 170	121 - 170
2	5	1	SER	SER	THR	THR	2	H	H	121 - 170	121 - 170
1	6	1	MET	MET	TYR	TYR	4	A	A	171 - 181	171 - 181
2	6	1	MET	MET	TYR	TYR	4	H	H	171 - 181	171 - 181
1	7	1	SER	SER	VAL	VAL	2	A	A	182 - 207	182 - 207
2	7	1	SER	SER	VAL	VAL	2	H	H	182 - 207	182 - 207
1	8	1	LEU	LEU	LEU	LEU	4	A	A	208 - 218	208 - 218
2	8	1	LEU	LEU	LEU	LEU	4	H	H	208 - 218	208 - 218
1	9	1	ALA	ALA	PHE	PHE	2	A	A	219 - 239	219 - 239
2	9	1	ALA	ALA	PHE	PHE	2	H	H	219 - 239	219 - 239
1	10	1	THR	THR	GLY	GLY	4	A	A	240 - 257	240 - 257
2	10	1	THR	THR	GLY	GLY	4	H	H	240 - 257	240 - 257
1	11	1	VAL	VAL	PRO	PRO	3	A	A	258 - 271	258 - 271
2	11	1	VAL	VAL	PRO	PRO	3	H	H	258 - 271	258 - 271
1	12	1	GLN	GLN	ARG	ARG	4	A	A	272 - 331	272 - 331
2	12	1	GLN	GLN	ARG	ARG	4	H	H	272 - 331	272 - 331
1	13	1	SER	SER	THR	THR	3	A	A	332 - 345	332 - 345
2	13	1	SER	SER	THR	THR	3	H	H	332 - 345	332 - 345
1	1	2	PHE	PHE	LEU	LEU	4	E	E	11 - 65	11 - 65
2	1	2	PHE	PHE	LEU	LEU	4	C	C	11 - 65	11 - 65
1	2	2	ARG	ARG	HIS	HIS	2	E	E	86 - 100	86 - 100
2	2	2	ARG	ARG	HIS	HIS	2	C	C	86 - 100	86 - 100
1	3	2	VAL	VAL	HIS	HIS	2	E	E	101 - 106	101 - 106
2	3	2	VAL	VAL	HIS	HIS	2	C	C	101 - 106	101 - 106
1	4	2	ASP	ASP	LYS	LYS	4	E	E	107 - 129	107 - 129
2	4	2	ASP	ASP	LYS	LYS	4	C	C	107 - 129	107 - 129
1	5	2	MET	MET	MET	MET	2	E	E	130 - 171	130 - 171
2	5	2	MET	MET	MET	MET	2	C	C	130 - 171	130 - 171
1	6	2	GLU	GLU	SER	SER	4	E	E	172 - 182	172 - 182
2	6	2	GLU	GLU	SER	SER	4	C	C	172 - 182	172 - 182
1	7	2	MET	MET	THR	THR	2	E	E	183 - 209	183 - 209
2	7	2	MET	MET	THR	THR	2	C	C	183 - 209	183 - 209
1	8	2	GLY	GLY	ALA	ALA	4	E	E	210 - 219	210 - 219
2	8	2	GLY	GLY	ALA	ALA	4	C	C	210 - 219	210 - 219
1	9	2	PHE	PHE	LEU	LEU	2	E	E	220 - 237	220 - 237
2	9	2	PHE	PHE	LEU	LEU	2	C	C	220 - 237	220 - 237
1	10	2	ASP	ASP	VAL	VAL	4	E	E	238 - 258	238 - 258
2	10	2	ASP	ASP	VAL	VAL	4	C	C	238 - 258	238 - 258
1	11	2	ILE	ILE	PHE	PHE	3	E	E	259 - 265	259 - 265
2	11	2	ILE	ILE	PHE	PHE	3	C	C	259 - 265	259 - 265
1	12	2	ALA	ALA	ILE	ILE	4	E	E	266 - 300	266 - 300
2	12	2	ALA	ALA	ILE	ILE	4	C	C	266 - 300	266 - 300
1	13	2	GLN	GLN	ILE	ILE	3	E	E	301 - 344	301 - 344
2	13	2	GLN	GLN	ILE	ILE	3	C	C	301 - 344	301 - 344
1	1	3	PRO	PRO	PRO	PRO	5	B	B	10 - 34	10 - 34
2	1	3	PRO	PRO	PRO	PRO	5	G	G	10 - 34	10 - 34
1	2	3	LYS	LYS	TYR	TYR	4	B	B	35 - 42	35 - 42
2	2	3	LYS	LYS	TYR	TYR	4	G	G	35 - 42	35 - 42
1	3	3	PHE	PHE	LYS	LYS	5	B	B	43 - 51	43 - 51
2	3	3	PHE	PHE	LYS	LYS	5	G	G	43 - 51	43 - 51
1	4	3	GLN	GLN	ASP	ASP	2	B	B	52 - 66	52 - 66
2	4	3	GLN	GLN	ASP	ASP	2	G	G	52 - 66	52 - 66
1	5	3	LEU	LEU	HIS	HIS	3	B	B	85 - 106	85 - 106
2	5	3	LEU	LEU	HIS	HIS	3	G	G	85 - 106	85 - 106
1	6	3	MET	MET	TYR	TYR	4	B	B	130 - 181	130 - 181
2	6	3	MET	MET	TYR	TYR	4	G	G	130 - 181	130 - 181
1	7	3	SER	SER	ALA	ALA	3	B	B	182 - 219	182 - 219
2	7	3	SER	SER	ALA	ALA	3	G	G	182 - 219	182 - 219
1	8	3	PHE	PHE	ILE	ILE	2	B	B	220 - 236	220 - 236
2	8	3	PHE	PHE	ILE	ILE	2	G	G	220 - 236	220 - 236
1	9	3	LEU	LEU	VAL	VAL	4	B	B	237 - 329	237 - 329
2	9	3	LEU	LEU	VAL	VAL	4	G	G	237 - 329	237 - 329
1	10	3	LYS	LYS	THR	THR	3	B	B	330 - 345	330 - 345
2	10	3	LYS	LYS	THR	THR	3	G	G	330 - 345	330 - 345
1	1	4	PRO	PRO	GLU	GLU	5	D	D	10 - 41	10 - 41
2	1	4	PRO	PRO	GLU	GLU	5	F	F	10 - 41	10 - 41
1	2	4	ARG	ARG	LEU	LEU	4	D	D	54 - 65	54 - 65
2	2	4	ARG	ARG	LEU	LEU	4	F	F	54 - 65	54 - 65
1	3	4	LEU	LEU	LEU	LEU	4	D	D	85 - 110	85 - 110
2	3	4	LEU	LEU	LEU	LEU	4	F	F	85 - 110	85 - 110
1	4	4	MET	MET	THR	THR	4	D	D	130 - 170	130 - 170
2	4	4	MET	MET	THR	THR	4	F	F	130 - 170	130 - 170
1	5	4	MET	MET	ARG	ARG	5	D	D	171 - 180	171 - 180
2	5	4	MET	MET	ARG	ARG	5	F	F	171 - 180	171 - 180
1	6	4	TYR	TYR	ALA	ALA	4	D	D	181 - 219	181 - 219
2	6	4	TYR	TYR	ALA	ALA	4	F	F	181 - 219	181 - 219
1	7	4	PHE	PHE	PHE	PHE	2	D	D	220 - 239	220 - 239
2	7	4	PHE	PHE	PHE	PHE	2	F	F	220 - 239	220 - 239
1	8	4	THR	THR	PRO	PRO	4	D	D	240 - 262	240 - 262
2	8	4	THR	THR	PRO	PRO	4	F	F	240 - 262	240 - 262
1	9	4	ILE	ILE	LEU	LEU	5	D	D	263 - 291	263 - 291
2	9	4	ILE	ILE	LEU	LEU	5	F	F	263 - 291	263 - 291
1	10	4	GLU	GLU	PRO	PRO	4	D	D	292 - 322	292 - 322
2	10	4	GLU	GLU	PRO	PRO	4	F	F	292 - 322	292 - 322
1	11	4	GLU	GLU	THR	THR	3	D	D	323 - 345	323 - 345
2	11	4	GLU	GLU	THR	THR	3	F	F	323 - 345	323 - 345

NCS ensembles :

ID
1
2
3
4

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	Geranyl diphosphate synthase Mass: 37844.316 Da / Num. of mol.: 8 / Fragment: residues in UNP 76-422 / Mutation: E178A,Q179A,E281A,K282A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AtNPPPS, gpps / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9FT89, UniProt: Q5HZ00*PLUS, heptaprenyl diphosphate synthase

#1: Protein

Geranyl diphosphate synthase

Mass: 37844.316 Da / Num. of mol.: 8 / Fragment: residues in UNP 76-422 / Mutation: E178A,Q179A,E281A,K282A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: AtNPPPS, gpps / Plasmid: pET32 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9FT89, UniProt: Q5HZ00*PLUS, heptaprenyl diphosphate synthase

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Non-polymers , 6 types, 719 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-FPP / FARNESYL DIPHOSPHATE Mass: 382.326 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₅H₂₈O₇P₂
#4: Chemical	ChemComp-ISY / 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid / Isopentyl S-Thiolodiphosphate Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₂O₆P₂S
#5: Chemical	ChemComp-PPV / PYROPHOSPHATE Mass: 177.975 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H₄O₇P₂
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.28 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / pH: 6 Details: 18%(w/v) PEG3350, 0.17M Sodium thiocyanate, pH 6.0, vapor diffusion, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-5A / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2009

Radiation

Monochromator: Horizontally Focusing Single Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.944
1	1	-H-K, K, -L	2	0.056

Reflection

Resolution: 2.65→30 Å / Num. obs: 83662 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / B_iso Wilson estimate: 78.8 Å² / R_merge(I) obs: 0.048 / Net I/σ(I): 28.3

Reflection shell

Resolution: 2.65→2.74 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.495 / Mean I/σ(I) obs: 2.1 / Num. unique all: 21336 / % possible all: 97.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
DENZO		data reduction
SCALEPACK		data scaling
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3APZ

3apz

Resolution: 2.65→30 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.908 / WR_factor R_free: 0.2721 / WR_factor R_work: 0.2224 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7657 / SU B: 25.823 / SU ML: 0.245 / SU R_free: 0.0799 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.274	4284	5.1 %	RANDOM
R_work	0.222	-	-	-
obs	0.2247	83456	98.57 %	-

Solvent computation

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

Displacement parameters

B_iso max: 132.01 Å² / B_iso mean: 77.543 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-24.33 Å²	0 Å²	0 Å²
2-	-	-24.33 Å²	0 Å²
3-	-	-	48.67 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19483	0	248	695	20426

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	19926
X-RAY DIFFRACTION	r_angle_refined_deg	1.472	1.992	26939
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.192	5	2529
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.942	23.812	821
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.18	15	3547
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.769	15	158
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	3268
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	14462
X-RAY DIFFRACTION	r_mcbond_it	0.459	1.5	12645
X-RAY DIFFRACTION	r_mcangle_it	0.907	2	20238
X-RAY DIFFRACTION	r_scbond_it	1.442	3	7281
X-RAY DIFFRACTION	r_scangle_it	2.521	4.5	6701

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	700	TIGHT POSITIONAL	0.03	0.05
1	A	1467	MEDIUM POSITIONAL	0.04	0.5
1	A	227	LOOSE POSITIONAL	0.05	5
1	A	700	TIGHT THERMAL	0.06	0.5
1	A	1467	MEDIUM THERMAL	0.06	2
1	A	227	LOOSE THERMAL	0.07	10
2	E	636	TIGHT POSITIONAL	0.03	0.05
2	E	1562	MEDIUM POSITIONAL	0.07	0.5
2	E	193	LOOSE POSITIONAL	0.05	5
2	E	636	TIGHT THERMAL	0.07	0.5
2	E	1562	MEDIUM THERMAL	0.07	2
2	E	193	LOOSE THERMAL	0.07	10
3	B	432	TIGHT POSITIONAL	0.04	0.05
3	B	1394	MEDIUM POSITIONAL	0.1	0.5
3	B	426	LOOSE POSITIONAL	0.11	5
3	B	432	TIGHT THERMAL	0.08	0.5
3	B	1394	MEDIUM THERMAL	0.09	2
3	B	426	LOOSE THERMAL	0.07	10
4	D	172	TIGHT POSITIONAL	0.03	0.05
4	D	1638	MEDIUM POSITIONAL	0.05	0.5
4	D	358	LOOSE POSITIONAL	0.06	5
4	D	172	TIGHT THERMAL	0.07	0.5
4	D	1638	MEDIUM THERMAL	0.09	2
4	D	358	LOOSE THERMAL	0.08	10

LS refinement shell

Resolution: 2.65→2.718 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.369	263	-
R_work	0.279	5597	-
all	-	5860	-
obs	-	21336	94.36 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.8689	-0.916	2.827	0.8137	-0.984	5.0192	-0.4194	0.492	0.8521	-0.1135	-0.1645	-0.2377	-0.5604	0.4813	0.5839	0.5085	-0.2075	-0.1398	0.3513	0.217	0.385	-46.705	33.599	3.949
2	3.2368	-1.3034	1.4127	1.2356	-0.77	0.9243	-0.0467	0.2603	-0.0608	-0.1166	0.0183	0.0614	0.1327	0.048	0.0285	0.4913	-0.0685	-0.027	0.4637	0.0636	0.0564	-29.293	8.697	23.146
3	4.0822	1.625	0.5102	2.4043	0.5465	2.0749	0.1002	-0.4258	0.238	0.4299	-0.2814	-0.0626	-0.1886	-0.1667	0.1812	0.4003	-0.0774	-0.0588	0.379	-0.0214	0.0448	-79.156	20.097	1.747
4	1.6638	0.7665	1.111	1.4515	0.3251	0.93	0.1629	-0.1152	-0.2829	0.2477	-0.0381	-0.2066	0.1279	0.1108	-0.1247	0.4358	-0.0645	0.0036	0.6506	-0.082	0.117	-96.039	-8.67	-10.611
5	3.6032	1.6507	-0.1723	2.4606	-0.8301	1.896	0.0336	-0.3333	-0.4158	0.3703	-0.3122	-0.1637	0.2159	0.1298	0.2785	0.4079	-0.1024	0.0703	0.4238	-0.0138	0.4033	-40.657	-25.723	-1.548
6	1.9932	0.7394	-1.6859	1.0628	-0.6372	1.5674	0.1567	-0.2668	-0.1862	0.1536	-0.2207	0.095	-0.2265	-0.0253	0.064	0.4724	-0.032	-0.0196	0.6212	0.1051	0.2555	-24.601	3.414	-13.768
7	2.2804	-0.8876	-1.1341	1.3719	0.3849	1.0586	-0.0246	0.2385	-0.1009	-0.1119	-0.0006	-0.1513	-0.0951	-0.0181	0.0253	0.4453	-0.0449	0.0098	0.3755	-0.0739	0.1065	-87.677	-15.912	24.955
8	2.5869	-0.7046	-2.3875	1.0549	1.1345	5.2322	-0.3371	0.5976	-0.6321	-0.1461	-0.1494	0.1059	0.494	-0.6009	0.4864	0.5395	-0.2513	0.1619	0.4214	-0.2564	0.4464	-72.689	-39.179	2.787

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 348
2	X-RAY DIFFRACTION	2	B	9 - 348
3	X-RAY DIFFRACTION	3	C	6 - 347
4	X-RAY DIFFRACTION	4	D	8 - 348
5	X-RAY DIFFRACTION	5	E	8 - 347
6	X-RAY DIFFRACTION	6	F	9 - 348
7	X-RAY DIFFRACTION	7	G	8 - 348
8	X-RAY DIFFRACTION	8	H	8 - 347

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