PDB-2ifu: Crystal Structure of a Gamma-SNAP from Danio rerio

ID or keywords:

Entry

Database: PDB / ID: 2ifu

Title

Crystal Structure of a Gamma-SNAP from Danio rerio

Components

gamma-snap

Keywords

ENDOCYTOSIS/EXOCYTOSIS / Gamma-SNAP / membrane fusion / SNARE complex disassembly / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG / ENDOCYTOSIS-EXOCYTOSIS COMPLEX

Function / homology

Function and homology information

vesicle-mediated transport / intracellular protein transport / Golgi apparatus / membrane
Similarity search - Function

Biological species

Danio rerio (zebrafish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.6 Å

Authors

Bitto, E. / Wesenberg, G.E. / Phillips Jr., G.N. / Mccoy, J.G. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: Proteins / Year: 2008
Title: Structure and dynamics of gamma-SNAP: insight into flexibility of proteins from the SNAP family.
Authors: Bitto, E. / Bingman, C.A. / Kondrashov, D.A. / McCoy, J.G. / Bannen, R.M. / Wesenberg, G.E. / Phillips, G.N.

History

Deposition	Sep 21, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 10, 2006	Provider: repository / Type: Initial release
Revision 1.1	Jan 15, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Nov 13, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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	2ifu.cif.gz	226.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2ifu.ent.gz	180.8 KB	Display	PDB format
PDBx/mmJSON format	2ifu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2ifu_validation.pdf.gz	489.6 KB	Display	wwPDB validaton report
Full document	2ifu_full_validation.pdf.gz	544.1 KB	Display
Data in XML	2ifu_validation.xml.gz	43.5 KB	Display
Data in CIF	2ifu_validation.cif.gz	56.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/if/2ifu ftp://data.pdbj.org/pub/pdb/validation_reports/if/2ifu	HTTPS FTP

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Related structure data

Similar structure data	3opu-5 2wza-d 3opu-1 4ofq-2 3opu-2 2wqs-d 3opu-4 1edy-d 2l26-d 5dz9-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: GO.79361

Similar structure data

Other databases

TargetDB: GO.79361

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: gamma-snap

B: gamma-snap

C: gamma-snap

D: gamma-snap

hetero molecules

139 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: gamma-snap

hetero molecules

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

2

B: gamma-snap

hetero molecules

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

3

C: gamma-snap

hetero molecules

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

4

D: gamma-snap

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.378, 90.813, 264.173
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 4

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	PRO	PRO	A	A	107 - 275	109 - 277
2	1	ASN	ASN	PRO	PRO	B	B	107 - 275	109 - 277
1	2	ASN	ASN	PRO	PRO	A	A	107 - 275	109 - 277
2	2	ASN	ASN	PRO	PRO	C	C	107 - 275	109 - 277
1	3	ASN	ASN	PRO	PRO	A	A	107 - 275	109 - 277
2	3	ASN	ASN	PRO	PRO	D	D	107 - 275	109 - 277
1	4	ALA	ALA	TYR	TYR	A	A	1 - 96	3 - 98
2	4	ALA	ALA	TYR	TYR	B	B	1 - 96	3 - 98
1	5	PRO	PRO	TYR	TYR	A	A	28 - 96	30 - 98
2	5	PRO	PRO	TYR	TYR	C	C	28 - 96	30 - 98
1	6	TRP	TRP	TYR	TYR	A	A	26 - 96	28 - 98
2	6	TRP	TRP	TYR	TYR	D	D	26 - 96	28 - 98
1	7	ILE	ILE	GLU	GLU	A	A	97 - 106	99 - 108
2	7	ILE	ILE	GLU	GLU	B	B	97 - 106	99 - 108
1	8	ILE	ILE	GLU	GLU	A	A	97 - 106	99 - 108
2	8	ILE	ILE	GLU	GLU	C	C	97 - 106	99 - 108
1	9	ILE	ILE	GLU	GLU	A	A	97 - 106	99 - 108
2	9	ILE	ILE	GLU	GLU	D	D	97 - 106	99 - 108
1	10	LYS	LYS	SER	SER	A	A	4 - 22	6 - 24
2	10	LYS	LYS	SER	SER	C	C	4 - 22	6 - 24
1	11	SER	SER	SER	SER	A	A	6 - 22	8 - 24
2	11	SER	SER	SER	SER	D	D	6 - 22	8 - 24

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11

#1: Protein	gamma-snap Mass: 34585.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: zgc:110177 / Plasmid: PVP 33K / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 P(RARE2) / References: UniProt: Q5BJK3
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	3.61	66.3
2

Crystal grow

Temperature (K)	Crystal-ID	Method	Details
277	1	vapor diffusion, hanging drop	Protein Solution (10 MG/ML protein, 0.250 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M BisTris pH 7.0) mixed in a 1:1 ratio with the Well Solution (15% PEG 8K, 0.020 M lithium sulfate, 0.066 M PIPES pH 6.5, 0.034 M MOPS pH 7.0) Cryoprotected with Well Solution supplemented with up to 25% ethylene glycol, vapor diffusion, hanging drop, temperature 277K
277	2	vapor diffusion, hanging drop	Protein Solution (10 MG/ML protein, 0.250 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M BisTris pH 7.0) mixed in a 1:1 ratio with the Well Solution (7% PEG 8K, 0.20 M ammonium sulfate, 0.10 M MOPS pH 7) Cryoprotected with 15% PEG 8K, 0.100 M lithium sulfate, 0.10 M PIPES pH 6.5 up to 25% ethylene glycol, vapor diffusion, hanging drop, temperature 277K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	23-ID-D	1	0.97926
SYNCHROTRON	APS	22-ID	2	0.97925,0.96403

Detector

Type	ID	Detector	Date	Details
MARMOSAIC 300 mm CCD	1	CCD	Aug 24, 2006	Adjustable focusing mirrors in K-B geometry
MARMOSAIC 300 mm CCD	2	CCD	Aug 4, 2006	Horizontal sagitally focusing 2nd bent monochromator crystal, vertical bent focusing mirror

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si(111) Double Crystal Monochromater	SINGLE WAVELENGTH	M	x-ray	1
2	Cryogenically cooled Si (220) double bounce	MAD	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97926	1
2	0.97925	1
3	0.96403	1

Reflection

Resolution: 2.4→40.053 Å / Num. obs: 70210 / % possible obs: 88.3 % / Redundancy: 9.8 % / R_merge(I) obs: 0.093 / Χ²: 1.367 / Net I/σ(I): 11.759

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
2.4-2.46	3.4	0.568	1.19	2812	1.184	53.4
2.46-2.52	3.9	0.453		2956	1.209	56.7
2.52-2.59	4.5	0.489		3447	1.006	66.4
2.59-2.66	5.5	0.483		3898	1.011	74.4
2.66-2.75	6.5	0.424		4346	1.001	83.1
2.75-2.85	7.9	0.387		4898	1.017	93.3
2.85-2.96	9.6	0.357		5152	0.972	98.3
2.96-3.09	11	0.266		5263	1.055	99.6
3.09-3.26	12.3	0.213		5245	1.06	99.7
3.26-3.46	12.4	0.14		5261	1.151	99.8
3.46-3.73	12.4	0.095		5297	1.251	99.8
3.73-4.1	12.3	0.078		5308	1.43	99.8
4.1-4.7	12.3	0.068		5325	1.409	99.7
4.7-5.92	12.1	0.079		5431	2.095	99.9
5.92-40.05	11.3	0.068		5571	2.324	98.5

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Phasing

Phasing

Method:

MAD

Phasing MAD set

Highest resolution: 3.5 Å / Lowest resolution: 45.1 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	22869	3224
ISO_2	0.769	0.703	1.117	0.866	22864	3213
ANO_1	0.482	0	2.404	0	22844	0
ANO_2	0.531	0	2.431	0	22846	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	14.83-45.1	0	0	0	0	220	138
ISO_1	10.78-14.83	0	0	0	0	438	160
ISO_1	8.89-10.78	0	0	0	0	572	166
ISO_1	7.73-8.89	0	0	0	0	690	162
ISO_1	6.94-7.73	0	0	0	0	795	170
ISO_1	6.35-6.94	0	0	0	0	890	167
ISO_1	5.88-6.35	0	0	0	0	972	168
ISO_1	5.51-5.88	0	0	0	0	1052	164
ISO_1	5.2-5.51	0	0	0	0	1107	158
ISO_1	4.94-5.2	0	0	0	0	1180	161
ISO_1	4.71-4.94	0	0	0	0	1264	167
ISO_1	4.51-4.71	0	0	0	0	1307	165
ISO_1	4.33-4.51	0	0	0	0	1353	157
ISO_1	4.18-4.33	0	0	0	0	1420	155
ISO_1	4.04-4.18	0	0	0	0	1491	172
ISO_1	3.91-4.04	0	0	0	0	1527	164
ISO_1	3.79-3.91	0	0	0	0	1565	150
ISO_1	3.69-3.79	0	0	0	0	1651	163
ISO_1	3.59-3.69	0	0	0	0	1666	167
ISO_1	3.5-3.59	0	0	0	0	1709	150
ANO_1	14.83-45.1	0.427	0	2.439	0	214	0
ANO_1	10.78-14.83	0.397	0	2.832	0	438	0
ANO_1	8.89-10.78	0.481	0	2.542	0	572	0
ANO_1	7.73-8.89	0.393	0	3.177	0	690	0
ANO_1	6.94-7.73	0.381	0	3.23	0	795	0
ANO_1	6.35-6.94	0.369	0	3.289	0	890	0
ANO_1	5.88-6.35	0.367	0	3.322	0	972	0
ANO_1	5.51-5.88	0.353	0	3.608	0	1052	0
ANO_1	5.2-5.51	0.397	0	3.104	0	1106	0
ANO_1	4.94-5.2	0.459	0	2.675	0	1177	0
ANO_1	4.71-4.94	0.499	0	2.449	0	1261	0
ANO_1	4.51-4.71	0.532	0	2.187	0	1307	0
ANO_1	4.33-4.51	0.551	0	2.144	0	1353	0
ANO_1	4.18-4.33	0.58	0	1.916	0	1419	0
ANO_1	4.04-4.18	0.589	0	1.904	0	1488	0
ANO_1	3.91-4.04	0.637	0	1.603	0	1525	0
ANO_1	3.79-3.91	0.668	0	1.496	0	1564	0
ANO_1	3.69-3.79	0.699	0	1.352	0	1651	0
ANO_1	3.59-3.69	0.729	0	1.212	0	1664	0
ANO_1	3.5-3.59	0.773	0	1.07	0	1706	0
ISO_2	14.83-45.1	0.593	0.533	1.455	1.454	216	129
ISO_2	10.78-14.83	0.602	0.635	1.685	1.14	438	159
ISO_2	8.89-10.78	0.738	0.679	1.479	0.864	572	165
ISO_2	7.73-8.89	0.71	0.69	1.761	1.069	690	162
ISO_2	6.94-7.73	0.694	0.664	1.611	0.949	795	170
ISO_2	6.35-6.94	0.738	0.684	1.61	1.034	890	167
ISO_2	5.88-6.35	0.729	0.699	1.575	1.009	972	168
ISO_2	5.51-5.88	0.719	0.647	1.543	0.997	1052	164
ISO_2	5.2-5.51	0.76	0.734	1.464	1.095	1107	158
ISO_2	4.94-5.2	0.774	0.728	1.19	0.802	1180	161
ISO_2	4.71-4.94	0.847	0.737	0.836	0.735	1264	167
ISO_2	4.51-4.71	0.825	0.786	0.934	0.606	1307	165
ISO_2	4.33-4.51	0.832	0.781	0.853	0.495	1353	157
ISO_2	4.18-4.33	0.834	0.854	0.774	0.45	1420	155
ISO_2	4.04-4.18	0.842	0.799	0.733	0.429	1491	172
ISO_2	3.91-4.04	0.839	0.798	0.656	0.394	1527	164
ISO_2	3.79-3.91	0.85	0.824	0.63	0.456	1565	150
ISO_2	3.69-3.79	0.835	0.879	0.596	0.356	1651	163
ISO_2	3.59-3.69	0.827	0.789	0.532	0.33	1666	167
ISO_2	3.5-3.59	0.822	0.812	0.475	0.313	1708	150
ANO_2	14.83-45.1	0.364	0	3.277	0	211	0
ANO_2	10.78-14.83	0.558	0	1.983	0	438	0
ANO_2	8.89-10.78	0.484	0	2.845	0	572	0
ANO_2	7.73-8.89	0.384	0	3.761	0	690	0
ANO_2	6.94-7.73	0.359	0	3.939	0	795	0
ANO_2	6.35-6.94	0.347	0	3.962	0	890	0
ANO_2	5.88-6.35	0.364	0	3.885	0	972	0
ANO_2	5.51-5.88	0.352	0	4.195	0	1052	0
ANO_2	5.2-5.51	0.41	0	3.549	0	1107	0
ANO_2	4.94-5.2	0.464	0	3.174	0	1177	0
ANO_2	4.71-4.94	0.517	0	2.783	0	1261	0
ANO_2	4.51-4.71	0.566	0	2.495	0	1307	0
ANO_2	4.33-4.51	0.587	0	2.323	0	1353	0
ANO_2	4.18-4.33	0.656	0	1.955	0	1420	0
ANO_2	4.04-4.18	0.678	0	1.833	0	1489	0
ANO_2	3.91-4.04	0.76	0	1.382	0	1526	0
ANO_2	3.79-3.91	0.754	0	1.412	0	1564	0
ANO_2	3.69-3.79	0.808	0	1.25	0	1651	0
ANO_2	3.59-3.69	0.84	0	1.035	0	1665	0
ANO_2	3.5-3.59	0.874	0	0.955	0	1706	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	13.955	89.948	189.293	SE	71.19	2.01
2	19.521	36.669	148.211	SE	139.34	1.83
3	18.331	21.65	158.028	SE	193.2	1.68
4	4.107	24.512	238.743	SE	176.89	2.91
5	3.822	32.097	256.469	SE	53.62	0.75
6	3.554	17.479	109.221	SE	120.5	1.27
7	17.841	71.083	20.945	SE	300	3.45
8	2.854	89.997	148.748	SE	161.18	2.59
9	3.311	87.234	248.938	SE	180.43	2.16
10	1.263	34.206	60.28	SE	62.59	2.3
11	20.29	1.988	199.016	SE	41.61	1.74
12	13.774	75.255	148.445	SE	64	2.63
13	2.589	27.805	64.405	SE	74.6	2.12
14	2.483	24.862	4.731	SE	69.36	1.92
15	5.884	-0.437	136.015	SE	80.53	2.26
16	19.537	90.397	71.261	SE	70.53	2.21
17	15.851	24.686	29.101	SE	100.47	2.59
18	4.867	-0.236	141.234	SE	62.3	1.74
19	6.509	18.269	37.972	SE	77.52	1.82
20	7.263	68.23	82.568	SE	94.18	2.88
21	10.014	6.167	54.593	SE	101.28	2.85
22	16.446	-0.274	233.284	SE	148.52	2.2
23	8.274	20.731	1.89	SE	55.12	1.03
24	8.846	2.455	152.461	SE	95.64	2.08
25	14.568	34.158	12.826	SE	113.76	2.5
26	2.298	17.823	233.864	SE	110.75	1.56
27	18.288	-0.729	238.257	SE	212.28	3.27
28	18.664	4.438	191.854	SE	146.33	2.14
29	10.175	79.469	59.731	SE	274.97	4.41
30	79.107	62.797	27.93	SE	226.29	2.21
31	9.397	22.72	1.732	SE	67.86	1.09
32	62.848	55.037	18.514	SE	190.5	1.59
33	57.467	19.929	41.395	SE	71.16	1.21
34	62.275	9.298	48.635	SE	126.82	1.05
35	63.471	51.799	16.071	SE	214.48	1.79
36	46.148	13.995	12.112	SE	261.1	2.35
37	56.789	18.363	39.92	SE	65.07	1.45
38	44.466	25.807	29.771	SE	77.72	0.94
39	62.449	46.032	18.867	SE	300	2.51

Phasing dm

FOM : 0.58 / FOM acentric: 0.58 / FOM centric: 0.6 / Reflection: 53398 / Reflection acentric: 48290 / Reflection centric: 5108

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
7.7-45.812	0.97	0.98	0.94	2587	1955	632
4.8-7.7	0.91	0.93	0.8	7705	6634	1071
3.8-4.8	0.87	0.88	0.74	9484	8512	972
3.4-3.8	0.7	0.71	0.59	9483	8668	815
2.9-3.4	0.34	0.34	0.31	16276	15093	1183
2.7-2.9	0.14	0.14	0.16	7863	7428	435

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
RESOLVE	2.06	phasing
REFMAC	5.2.0005	refinement
PDB_EXTRACT	2	data extraction
HKL-2000		data reduction
PHENIX		phasing
SHELXD		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.6→40.053 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.92 / WR_factor R_free: 0.258 / WR_factor R_work: 0.241 / SU B: 22.64 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.261	3047	5.062 %	RANDOM
R_work	0.239	-	-	-
obs	0.24	60191	96.072 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 70.106 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.692 Å²	0 Å²	0 Å²
2-	-	2.414 Å²	0 Å²
3-	-	-	-0.722 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→40.053 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8644	0	50	64	8758

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	8835
X-RAY DIFFRACTION	r_angle_refined_deg	1.469	1.972	11901
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.507	5	1094
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.4	25.211	426
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.433	15	1639
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.797	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	1278
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6636
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	4025
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	6089
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	200
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.319	0.2	108
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.249	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	0.707	1.5	5576
X-RAY DIFFRACTION	r_mcangle_it	1.184	2	8689
X-RAY DIFFRACTION	r_scbond_it	1.998	3	3619
X-RAY DIFFRACTION	r_scangle_it	3.223	4.5	3209

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	1333	MEDIUM POSITIONAL	0.11	0.05
1	1333	MEDIUM THERMAL	1.06	2
2	1323	MEDIUM POSITIONAL	0.07	0.05
2	1323	MEDIUM THERMAL	1.09	2
3	1323	MEDIUM POSITIONAL	0.05	0.05
3	1323	MEDIUM THERMAL	1.03	2
4	758	MEDIUM POSITIONAL	0.09	0.05
4	758	MEDIUM THERMAL	1.24	2
5	535	MEDIUM POSITIONAL	0.04	0.05
5	535	MEDIUM THERMAL	0.94	2
6	558	MEDIUM POSITIONAL	0.04	0.05
6	558	MEDIUM THERMAL	0.86	2
7	80	MEDIUM POSITIONAL	0.12	0.05
7	80	MEDIUM THERMAL	1.3	2
8	80	MEDIUM POSITIONAL	0.05	0.05
8	80	MEDIUM THERMAL	0.76	2
9	80	MEDIUM POSITIONAL	0.05	0.05
9	80	MEDIUM THERMAL	0.6	2
10	153	MEDIUM POSITIONAL	0.04	0.05
10	153	MEDIUM THERMAL	0.93	2
11	136	MEDIUM POSITIONAL	0.04	0.05
11	136	MEDIUM THERMAL	0.88	2

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.6-2.668	0.422	169	0.4	3286	4556	75.834
2.668-2.741	0.405	210	0.343	3530	4480	83.482
2.741-2.82	0.336	202	0.339	3759	4294	92.245
2.82-2.907	0.341	226	0.312	3862	4210	97.102
2.907-3.002	0.274	210	0.259	3868	4113	99.149
3.002-3.107	0.268	208	0.232	3721	3943	99.645
3.107-3.225	0.301	193	0.251	3638	3840	99.766
3.225-3.356	0.288	183	0.25	3487	3675	99.864
3.356-3.505	0.274	182	0.246	3376	3564	99.832
3.505-3.676	0.234	166	0.236	3185	3356	99.851
3.676-3.875	0.256	144	0.235	3097	3242	99.969
3.875-4.11	0.228	137	0.224	2942	3083	99.87
4.11-4.393	0.225	142	0.213	2741	2890	99.758
4.393-4.745	0.235	138	0.201	2563	2704	99.889
4.745-5.197	0.23	134	0.222	2348	2482	100
5.197-5.809	0.313	126	0.265	2144	2270	100
5.809-6.706	0.267	92	0.239	1918	2010	100
6.706-8.208	0.263	86	0.234	1664	1751	99.943
8.208-11.585	0.183	63	0.169	1293	1368	99.123
11.585-132.453	0.206	36	0.26	722	821	92.326

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