PDB-3hty: Crystal structure of a lipocalin-like protein (BT_0869) from Bact...

Basic information

• Entry: Database: PDB / ID: 3hty
• Title: Crystal structure of a lipocalin-like protein (BT_0869) from Bacteroides thetaiotaomicron VPI-5482 at 1.95 A resolution
• Components: hypothetical protein BT_0869Hypothesis
• Keywords: structural genomics / unknown function / NP_809782.1 / hypothetical protein BT_0869 from Bacteroides thetaiotaomicron VPI-5482 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
• Function / homology: Lipocalin-like / Lipocalin - #280 / Lipocalin-like domain / Lipocalin / Beta Barrel / Mainly Beta / Lipocalin-like domain-containing protein
• Biological species: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
• Authors: Joint Center for Structural Genomics / Joint Center for Structural Genomics (JCSG)
• Citation: Journal: To be Published; Title: Crystal structure of hypothetical protein BT_0869 from Bacteroides thetaiotaomicron VPI-5482 (NP_809782.1) at 1.95 A resolution; Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Jun 12, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 7, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Dec 24, 2014	Group: Structure summary
Revision 1.3	Oct 25, 2017	Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.4	Jul 24, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5	Feb 1, 2023	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: hypothetical protein BT_0869

B: hypothetical protein BT_0869

C: hypothetical protein BT_0869

D: hypothetical protein BT_0869

E: hypothetical protein BT_0869

F: hypothetical protein BT_0869

G: hypothetical protein BT_0869

H: hypothetical protein BT_0869

I: hypothetical protein BT_0869

J: hypothetical protein BT_0869

K: hypothetical protein BT_0869

L: hypothetical protein BT_0869

M: hypothetical protein BT_0869

N: hypothetical protein BT_0869

O: hypothetical protein BT_0869

P: hypothetical protein BT_0869

hetero molecules

Summary:

• 171 kDa, 16 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	170,727	75
Polymers	165,218	16
Non-polymers	5,509	59
Water	26,266	1458

1

A: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.5 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,510	3
Polymers	10,326	1
Non-polymers	184	2
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

2

B: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.6 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,602	4
Polymers	10,326	1
Non-polymers	276	3
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

3

C: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.8 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,791	6
Polymers	10,326	1
Non-polymers	464	5
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

4

D: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.5 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,514	3
Polymers	10,326	1
Non-polymers	188	2
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

5

E: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.5 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,510	3
Polymers	10,326	1
Non-polymers	184	2
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

6

F: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 11 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,979	8
Polymers	10,326	1
Non-polymers	653	7
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

7

G: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.5 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,514	3
Polymers	10,326	1
Non-polymers	188	2
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

8

H: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.8 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,795	6
Polymers	10,326	1
Non-polymers	468	5
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

9

I: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,702	5
Polymers	10,326	1
Non-polymers	376	4
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

10

J: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.8 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,791	6
Polymers	10,326	1
Non-polymers	464	5
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

11

K: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.8 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,798	6
Polymers	10,326	1
Non-polymers	472	5
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

12

L: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.6 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,606	4
Polymers	10,326	1
Non-polymers	280	3
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

13

M: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.5 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,510	3
Polymers	10,326	1
Non-polymers	184	2
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

14

N: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.8 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,795	6
Polymers	10,326	1
Non-polymers	468	5
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

15

O: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.8 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,795	6
Polymers	10,326	1
Non-polymers	468	5
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

16

P: hypothetical protein BT_0869

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 10.5 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,514	3
Polymers	10,326	1
Non-polymers	188	2
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Unit cell

Length a, b, c (Å)	125.510, 125.510, 181.450
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3121

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
11	1	K
12	1	L
13	1	M
14	1	N
15	1	O
16	1	P

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	1 - 33
2	1	1	4	B	1 - 33
3	1	1	4	C	1 - 33
4	1	1	4	D	1 - 33
5	1	1	4	E	1 - 33
6	1	1	4	F	1 - 33
7	1	1	4	G	1 - 33
8	1	1	4	H	1 - 33
9	1	1	4	I	1 - 33
10	1	1	4	J	1 - 33
11	1	1	4	K	1 - 33
12	1	1	4	L	1 - 33
13	1	1	4	M	1 - 33
14	1	1	4	N	1 - 33
15	1	1	4	O	1 - 33
16	1	1	4	P	1 - 33
1	2	1	6	A	34 - 39
2	2	1	6	B	34 - 39
3	2	1	6	C	34 - 39
4	2	1	6	D	34 - 39
5	2	1	6	E	34 - 39
6	2	1	6	F	34 - 39
7	2	1	6	G	34 - 39
8	2	1	6	H	34 - 39
9	2	1	6	I	34 - 39
10	2	1	6	J	34 - 39
11	2	1	6	K	34 - 39
12	2	1	6	L	34 - 39
13	2	1	6	M	34 - 39
14	2	1	6	N	34 - 39
15	2	1	6	O	34 - 39
16	2	1	6	P	34 - 39
1	3	1	4	A	40 - 56
2	3	1	4	B	40 - 56
3	3	1	4	C	40 - 56
4	3	1	4	D	40 - 56
5	3	1	4	E	40 - 56
6	3	1	4	F	40 - 56
7	3	1	4	G	40 - 56
8	3	1	4	H	40 - 56
9	3	1	4	I	40 - 56
10	3	1	4	J	40 - 56
11	3	1	4	K	40 - 56
12	3	1	4	L	40 - 56
13	3	1	4	M	40 - 56
14	3	1	4	N	40 - 56
15	3	1	4	O	40 - 56
16	3	1	4	P	40 - 56
1	4	1	6	A	57 - 60
2	4	1	6	B	57 - 60
3	4	1	6	C	57 - 60
4	4	1	6	D	57 - 60
5	4	1	6	E	57 - 60
6	4	1	6	F	57 - 60
7	4	1	6	G	57 - 60
8	4	1	6	H	57 - 60
9	4	1	6	I	57 - 60
10	4	1	6	J	57 - 60
11	4	1	6	K	57 - 60
12	4	1	6	L	57 - 60
13	4	1	6	M	57 - 60
14	4	1	6	N	57 - 60
15	4	1	6	O	57 - 60
16	4	1	6	P	57 - 60
1	5	1	4	A	61 - 66
2	5	1	4	B	61 - 66
3	5	1	4	C	61 - 66
4	5	1	4	D	61 - 66
5	5	1	4	E	61 - 66
6	5	1	4	F	61 - 66
7	5	1	4	G	61 - 66
8	5	1	4	H	61 - 66
9	5	1	4	I	61 - 66
10	5	1	4	J	61 - 66
11	5	1	4	K	61 - 66
12	5	1	4	L	61 - 66
13	5	1	4	M	61 - 66
14	5	1	4	N	61 - 66
15	5	1	4	O	61 - 66
16	5	1	4	P	61 - 66
1	6	1	6	A	67 - 69
2	6	1	6	B	67 - 69
3	6	1	6	C	67 - 69
4	6	1	6	D	67 - 69
5	6	1	6	E	67 - 69
6	6	1	6	F	67 - 69
7	6	1	6	G	67 - 69
8	6	1	6	H	67 - 69
9	6	1	6	I	67 - 69
10	6	1	6	J	67 - 69
11	6	1	6	K	67 - 69
12	6	1	6	L	67 - 69
13	6	1	6	M	67 - 69
14	6	1	6	N	67 - 69
15	6	1	6	O	67 - 69
16	6	1	6	P	67 - 69
1	7	1	4	A	70 - 75
2	7	1	4	B	70 - 75
3	7	1	4	C	70 - 75
4	7	1	4	D	70 - 75
5	7	1	4	E	70 - 75
6	7	1	4	F	70 - 75
7	7	1	4	G	70 - 75
8	7	1	4	H	70 - 75
9	7	1	4	I	70 - 75
10	7	1	4	J	70 - 75
11	7	1	4	K	70 - 75
12	7	1	4	L	70 - 75
13	7	1	4	M	70 - 75
14	7	1	4	N	70 - 75
15	7	1	4	O	70 - 75
16	7	1	4	P	70 - 75
1	8	1	6	A	76 - 85
2	8	1	6	B	76 - 85
3	8	1	6	C	76 - 85
4	8	1	6	D	76 - 85
5	8	1	6	E	76 - 85
6	8	1	6	F	76 - 85
7	8	1	6	G	76 - 85
8	8	1	6	H	76 - 85
9	8	1	6	I	76 - 85
10	8	1	6	J	76 - 85
11	8	1	6	K	76 - 85
12	8	1	6	L	76 - 85
13	8	1	6	M	76 - 85
14	8	1	6	N	76 - 85
15	8	1	6	O	76 - 85
16	8	1	6	P	76 - 85
1	9	1	4	A	86 - 102
2	9	1	4	B	86 - 102
3	9	1	4	C	86 - 102
4	9	1	4	D	86 - 102
5	9	1	4	E	86 - 102
6	9	1	4	F	86 - 102
7	9	1	4	G	86 - 102
8	9	1	4	H	86 - 102
9	9	1	4	I	86 - 102
10	9	1	4	J	86 - 102
11	9	1	4	K	86 - 102
12	9	1	4	L	86 - 102
13	9	1	4	M	86 - 102
14	9	1	4	N	86 - 102
15	9	1	4	O	86 - 102
16	9	1	4	P	86 - 102
1	10	1	6	A	103 - 115
2	10	1	6	B	103 - 115
3	10	1	6	C	103 - 115
4	10	1	6	D	103 - 115
5	10	1	6	E	103 - 115
6	10	1	6	F	103 - 115
7	10	1	6	G	103 - 115
8	10	1	6	H	103 - 115
9	10	1	6	I	103 - 115
10	10	1	6	J	103 - 115
11	10	1	6	K	103 - 115
12	10	1	6	L	103 - 115
13	10	1	6	M	103 - 115
14	10	1	6	N	103 - 115
15	10	1	6	O	103 - 115
16	10	1	6	P	103 - 115

• Details: ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF THE MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

Components

#1: Protein

A B C D E F G H I J K L M N O P
hypothetical protein BT_0869 / Hypothesis

Details:

Mass: 10326.101 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_0869, NP_809782.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A9E6

#2: Chemical

A-116 A-117 B-21 B-116 B-117 C-116 C-117 C-118 C-119 D-116 E-116 E-117 F-20 F-116 F-117 F-118 F-119 G-116 H-116 H-117 ...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol

Details:

Mass: 92.094 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C₃H₈O₃

#3: Chemical

C-11 D-4 F-3 F-10 G-19 H-6 H-16 I-8 I-13 J-12 K-2 K-9 K-15 L-17 N-7 N-18 O-1 O-5 P-14
ChemComp-SO4 / SULFATE ION / Sulfate

Details:

Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO₄

#4: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 1458 / Source method: isolated from a natural source / Formula: H₂O

• Sequence details: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 23-115 OF THE FULL LENGTH PROTEIN.

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.5 ų/Da / Density % sol: 50.74 %
• Crystal grow: Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 ; Details: 1.6000M (NH4)2SO4, 0.1M Citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97965
• Detector: Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2008 / Details: Adjustable focusing mirrors in K-B geometry
• Radiation: Monochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.94645	1
2	0.97965	1

• Reflection: Resolution: 1.95→29.735 Å / Num. obs: 120441 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / B_iso Wilson estimate: 23.792 Ų / R_merge F obs: 0.17 / R_merge(I) obs: 0.128 / R_rim(I) all: 0.141 / Net I/σ(I): 8.71 / Num. measured all: 672745

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Rmerge F obs	Rmerge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	Rrim(I) all	% possible all
1.95-2.01	0.787	0.891	2.1	57956	10368	10365	0.984	100
2.01-2.08	0.584	0.627	2.8	59497	10638	10628	0.692	99.9
2.08-2.17	0.449	0.489	3.5	65703	11751	11733	0.54	99.8
2.17-2.26	0.361	0.398	4.3	55769	9959	9945	0.439	99.9
2.26-2.38	0.303	0.327	5.1	62083	11078	11074	0.361	100
2.38-2.53	0.236	0.266	6.1	61927	11039	11027	0.293	99.9
2.53-2.73	0.172	0.198	7.8	63038	11223	11214	0.219	99.9
2.73-3	0.114	0.136	10.4	60773	10833	10819	0.15	99.9
3-3.43	0.067	0.088	14.4	61482	10997	10985	0.097	99.9
3.43-4.32	0.04	0.062	18.7	62362	11201	11190	0.069	99.9
4.32-29.735	0.039	0.061	19.4	62155	11561	11461	0.067	99.1

Phasing

• Phasing: Method: MAD

Processing

Software

Name	Version	Classification	NB
REFMAC	5.2.0019	refinement
PHENIX		refinement
SHELX		phasing
MolProbity	3beta29	model building
XSCALE		data scaling
PDB_EXTRACT	3.006	data extraction
XDS		data reduction
SHELXD		phasing
autoSHARP		phasing

Refinement

Method to determine structure: MAD / Resolution: 1.95→29.735 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.945 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 6.68 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.139
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.SULFATE (SO4) AND GLYCEROL (GOL) MOLECULES FROM CRYSTALLIZATON SOLUTIONS ARE ALSO MODELED IN THE STRUCTURE.

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.206	6044	5 %	RANDOM
Rwork	0.166	114337	-	-
obs	0.168	120381	99.83 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 102.68 Ų / B_iso mean: 38.121 Ų / B_iso min: 15.53 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.23 Å2	0.12 Å2	0 Å2
2-	-	0.23 Å2	0 Å2
3-	-	-	-0.35 Å2

Refinement step

Cycle: LAST / Resolution: 1.95→29.735 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11096	0	335	1458	12889

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	11870
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	7807
X-RAY DIFFRACTION	r_angle_refined_deg	1.641	1.989	16039
X-RAY DIFFRACTION	r_angle_other_deg	0.899	3	19371
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.499	5	1563
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.913	26.912	421
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.122	15	2122
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.936	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	1838
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	13094
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1999
X-RAY DIFFRACTION	r_nbd_refined	0.186	0.3	1617
X-RAY DIFFRACTION	r_nbd_other	0.181	0.3	8060
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.5	5547
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.5	6691
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.176	0.5	2066
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.114	0.5	6
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.221	0.3	51
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.209	0.3	119
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.196	0.5	127
X-RAY DIFFRACTION	r_symmetry_hbond_other	0.105	0.5	1
X-RAY DIFFRACTION	r_mcbond_it	1.834	3	8170
X-RAY DIFFRACTION	r_mcbond_other	0.554	3	3211
X-RAY DIFFRACTION	r_mcangle_it	2.512	5	12204
X-RAY DIFFRACTION	r_scbond_it	4.641	8	4722
X-RAY DIFFRACTION	r_scangle_it	6.264	11	3835

Refine LS restraints NCS

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

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	587	MEDIUM POSITIONAL	0.32	0.5
2	B	587	MEDIUM POSITIONAL	0.41	0.5
3	C	587	MEDIUM POSITIONAL	0.32	0.5
4	D	587	MEDIUM POSITIONAL	0.48	0.5
5	E	587	MEDIUM POSITIONAL	0.55	0.5
6	F	587	MEDIUM POSITIONAL	0.29	0.5
7	G	587	MEDIUM POSITIONAL	0.31	0.5
8	H	587	MEDIUM POSITIONAL	0.34	0.5
9	I	587	MEDIUM POSITIONAL	0.44	0.5
10	J	587	MEDIUM POSITIONAL	0.34	0.5
11	K	587	MEDIUM POSITIONAL	0.3	0.5
12	L	587	MEDIUM POSITIONAL	0.53	0.5
13	M	587	MEDIUM POSITIONAL	0.33	0.5
14	N	587	MEDIUM POSITIONAL	0.29	0.5
15	O	587	MEDIUM POSITIONAL	0.31	0.5
16	P	587	MEDIUM POSITIONAL	0.39	0.5
1	A	210	LOOSE POSITIONAL	1.49	5
2	B	210	LOOSE POSITIONAL	1.38	5
3	C	210	LOOSE POSITIONAL	1.53	5
4	D	210	LOOSE POSITIONAL	1.6	5
5	E	210	LOOSE POSITIONAL	1.78	5
6	F	210	LOOSE POSITIONAL	1.2	5
7	G	210	LOOSE POSITIONAL	1.07	5
8	H	210	LOOSE POSITIONAL	1.3	5
9	I	210	LOOSE POSITIONAL	1.19	5
10	J	210	LOOSE POSITIONAL	1.09	5
11	K	210	LOOSE POSITIONAL	0.92	5
12	L	210	LOOSE POSITIONAL	1.82	5
13	M	210	LOOSE POSITIONAL	1.3	5
14	N	210	LOOSE POSITIONAL	1.05	5
15	O	210	LOOSE POSITIONAL	1.35	5
16	P	210	LOOSE POSITIONAL	1.17	5
1	A	587	MEDIUM THERMAL	1.11	2
2	B	587	MEDIUM THERMAL	1.12	2
3	C	587	MEDIUM THERMAL	0.96	2
4	D	587	MEDIUM THERMAL	1.08	2
5	E	587	MEDIUM THERMAL	1.29	2
6	F	587	MEDIUM THERMAL	1.1	2
7	G	587	MEDIUM THERMAL	0.93	2
8	H	587	MEDIUM THERMAL	1.11	2
9	I	587	MEDIUM THERMAL	1.16	2
10	J	587	MEDIUM THERMAL	1.03	2
11	K	587	MEDIUM THERMAL	1.21	2
12	L	587	MEDIUM THERMAL	1.07	2
13	M	587	MEDIUM THERMAL	1.07	2
14	N	587	MEDIUM THERMAL	0.97	2
15	O	587	MEDIUM THERMAL	1.01	2
16	P	587	MEDIUM THERMAL	1.11	2
1	A	210	LOOSE THERMAL	3.84	10
2	B	210	LOOSE THERMAL	4.16	10
3	C	210	LOOSE THERMAL	3.33	10
4	D	210	LOOSE THERMAL	4.78	10
5	E	210	LOOSE THERMAL	5.87	10
6	F	210	LOOSE THERMAL	5.24	10
7	G	210	LOOSE THERMAL	3.68	10
8	H	210	LOOSE THERMAL	4.94	10
9	I	210	LOOSE THERMAL	3.7	10
10	J	210	LOOSE THERMAL	3.95	10
11	K	210	LOOSE THERMAL	4.44	10
12	L	210	LOOSE THERMAL	5.87	10
13	M	210	LOOSE THERMAL	5.95	10
14	N	210	LOOSE THERMAL	3.06	10
15	O	210	LOOSE THERMAL	4.21	10
16	P	210	LOOSE THERMAL	5.29	10

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.287	435	-
Rwork	0.219	8377	-
all	-	8812	-
obs	-	-	99.98 %

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	0.9716	0.3095	-0.206	1.7327	-0.2375	2.3937	0.0161	-0.1282	0.1234	0.0508	0.0194	0.0685	0.0149	-0.0296	-0.0355	-0.1817	-0.0071	0.0046	-0.1564	0.002	-0.1676	36.6985	31.3763	-3.7529
2	1.7131	0.1664	0.889	1.4105	0.8799	1.5478	0.0063	0.0363	-0.1206	-0.0825	0.0104	0.0418	0.1357	-0.1758	-0.0167	-0.1384	-0.0054	0.0067	-0.1485	0.0007	-0.1771	50.1372	42.8114	13.4513
3	2.1626	0.8859	-0.6419	1.692	0.1453	2.0524	-0.0015	0.1729	-0.0949	-0.3271	0.0042	-0.2465	0.0878	0.0558	-0.0027	-0.0987	0.0241	0.0401	-0.1525	-0.0146	-0.1135	71.4677	48.0142	7.6486
4	1.7712	-0.5728	0.458	3.3131	-0.3917	2.6299	0.0463	0.1445	-0.0787	-0.2331	0.0086	0.1024	-0.0144	-0.0534	-0.0549	-0.1877	0.0032	-0.0325	-0.1611	-0.0091	-0.173	66.122	24.1051	33.9909
5	2.1055	0.2933	0.1702	1.7646	-0.143	0.0879	0.0332	-0.1155	0.0916	0.1373	-0.0762	-0.0378	-0.1206	-0.1252	0.043	-0.017	0.0371	-0.0429	-0.0787	-0.0133	-0.0935	71.7841	46.2906	44.3066
6	2.4318	-1.3996	-1.3367	3.9454	1.9929	2.3986	-0.0501	-0.3803	0.1022	0.3709	0.2228	-0.423	0.0809	0.3415	-0.1728	-0.1172	0.0129	-0.0272	-0.0865	-0.044	-0.091	70.8902	64.8485	29.8962
7	2.099	-0.337	-0.5591	2.2255	1.084	1.4786	0.0748	0.0718	0.2133	-0.0748	-0.0929	0.1351	-0.1766	-0.1616	0.0181	-0.1212	0.042	-0.0061	-0.1198	-0.0228	-0.1262	48.5615	69.4164	22.3961
8	2.1184	0.2727	1.0755	3.0079	0.2506	1.7791	0.0004	0.2688	-0.0928	-0.3118	0.0074	0.2263	0.0172	-0.1131	-0.0077	-0.154	0.0027	-0.003	-0.1025	-0.0341	-0.1208	34.3693	78.2621	37.8386
9	1.9512	-0.3133	-0.0501	2.8671	-0.6791	1.6965	0.0339	0.2278	0.1558	-0.1279	-0.0595	0.1251	-0.2961	-0.0427	0.0256	-0.1387	0.0089	-0.0083	-0.1544	-0.0046	-0.1902	41.8852	99.2637	44.1236
10	2.5421	0.5995	1.1774	1.8555	0.0404	1.5466	-0.0958	0.0615	-0.0433	-0.0424	0.0403	-0.2256	-0.1458	0.1345	0.0555	-0.1356	-0.0098	0.0127	-0.1526	0.0063	-0.1639	65.2256	86.4068	51.2732
11	3.3811	-0.2116	1.2387	1.5842	-0.058	1.6336	-0.0491	-0.3201	-0.2104	0.1966	0.0646	0.1638	0.1305	-0.1115	-0.0155	-0.1317	0.016	0.0222	-0.1478	0.0091	-0.1374	49.8519	69.8962	59.1917
12	1.3687	-0.0109	-0.0907	2.1053	0.0303	0.4877	-0.082	0.0147	-0.1456	0.0199	0.0121	-0.0553	0.0464	0.1807	0.0699	-0.1202	0.0087	0.0273	-0.0682	0.0044	-0.1073	34.2246	77.6029	74.2644
13	1.8315	-0.1282	-0.172	1.9915	-0.0747	3.0999	-0.004	-0.1876	-0.1637	0.3714	-0.0711	-0.2222	0.0108	0.2229	0.0751	-0.0653	-0.0275	0.006	-0.1425	0.0165	-0.1439	39.785	116.1781	28.0858
14	2.4441	-0.7061	-1.419	1.5261	1.2354	2.213	0.0291	0.1252	0.1139	0.0887	-0.0303	0.0505	-0.1089	-0.2276	0.0012	-0.1347	0.0089	0.0138	-0.1264	-0.0144	-0.145	18.5025	122.9604	19.4004
15	2.5361	0.1772	-1.0874	1.6772	0.8771	2.1764	-0.0788	0.3238	-0.1371	-0.1872	-0.0785	0.0085	0.1712	0.0421	0.1573	-0.0963	0.0352	0.0546	-0.1219	-0.0203	-0.0856	40.7222	100.2945	5.6478
16	2.5914	1.8734	1.0499	2.7178	0.9897	2.3176	0.0862	-0.0186	-0.2028	0.0642	-0.0581	-0.0323	0.4028	-0.1057	-0.0281	-0.0931	-0.0384	0.0489	-0.121	-0.0363	-0.1139	18.5179	96.3383	10.1677

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	23 - 115
2	X-RAY DIFFRACTION	2	B	23 - 115
3	X-RAY DIFFRACTION	3	C	23 - 114
4	X-RAY DIFFRACTION	4	D	23 - 115
5	X-RAY DIFFRACTION	5	E	23 - 115
6	X-RAY DIFFRACTION	6	F	23 - 115
7	X-RAY DIFFRACTION	7	G	23 - 115
8	X-RAY DIFFRACTION	8	H	23 - 115
9	X-RAY DIFFRACTION	9	I	23 - 114
10	X-RAY DIFFRACTION	10	J	23 - 115
11	X-RAY DIFFRACTION	11	K	23 - 115
12	X-RAY DIFFRACTION	12	L	23 - 114
13	X-RAY DIFFRACTION	13	M	23 - 114
14	X-RAY DIFFRACTION	14	N	23 - 115
15	X-RAY DIFFRACTION	15	O	23 - 114
16	X-RAY DIFFRACTION	16	P	23 - 114