PDB-4apz: Structure of B. subtilis genomic dUTPase YncF in complex with dU,...

Basic information

• Entry: Database: PDB / ID: 4apz
• Title: Structure of B. subtilis genomic dUTPase YncF in complex with dU, PPi and Mg in P1
• Components: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF
• Keywords: HYDROLASE / YNCF

Function / homology

Function:

dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding

Domain/homology:

Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta

Component:

2'-DEOXYURIDINE / PHOSPHATE ION / PYROPHOSPHATE 2- / Deoxyuridine 5'-triphosphate nucleotidohydrolase YncF

• Biological species: BACILLUS SUBTILIS (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
• Authors: Garcia-Nafria, J. / Timm, J. / Harrison, C. / Turkenburg, J.P. / Wilson, K.S.
• Citation: Journal: Acta Crystallogr.,Sect.D / Year: 2013; Title: Tying Down the Arm in Bacillus Dutpase: Structure and Mechanism; Authors: Garcia-Nafria, J. / Timm, J. / Harrison, C. / Turkenburg, J.P. / Wilson, K.S.

History

Deposition	Apr 11, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 24, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2013	Group: Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.2	Jul 31, 2013	Group: Atomic model / Database references / Derived calculations / Other / Structure summary
Revision 1.3	Aug 7, 2013	Group: Database references
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_asym_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.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.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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

1: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

2: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

3: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

4: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

5: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

6: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

7: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

8: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

9: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

A: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

B: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

C: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

D: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

E: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

F: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

G: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

H: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

I: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

J: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

K: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

L: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

M: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

N: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

O: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

P: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

Q: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

R: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

S: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

T: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

U: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

V: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

W: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

X: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

Y: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

Z: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

a: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

b: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

c: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

d: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

e: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

f: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

g: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

h: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

i: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

j: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

k: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

l: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

m: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• 809 kDa, 48 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	809,481	194
Polymers	788,724	48
Non-polymers	20,756	146
Water	85,139	4726

1

k: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

l: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

m: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.7 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,676	13
Polymers	49,295	3
Non-polymers	1,380	10
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16340 Å2
ΔGint	-84.5 kcal/mol
Surface area	16090 Å2
Method	PISA

2

e: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

f: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

g: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.7 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,676	13
Polymers	49,295	3
Non-polymers	1,380	10
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16340 Å2
ΔGint	-82 kcal/mol
Surface area	15900 Å2
Method	PISA

3

1: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

Y: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

Z: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16080 Å2
ΔGint	-75.2 kcal/mol
Surface area	16110 Å2
Method	PISA

4

P: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

Q: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

R: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16120 Å2
ΔGint	-74.7 kcal/mol
Surface area	16310 Å2
Method	PISA

5

8: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

9: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

a: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	72	4

Symmetry operations:

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

Calculated values:

Buried area	16160 Å2
ΔGint	-74.5 kcal/mol
Surface area	16210 Å2
Method	PISA

6

S: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

T: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

U: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16120 Å2
ΔGint	-73.2 kcal/mol
Surface area	16180 Å2
Method	PISA

7

D: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

E: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

F: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16150 Å2
ΔGint	-75 kcal/mol
Surface area	16250 Å2
Method	PISA

8

A: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

B: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

C: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	72	4

Symmetry operations:

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

Calculated values:

Buried area	16180 Å2
ΔGint	-74.7 kcal/mol
Surface area	16240 Å2
Method	PISA

9

h: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

i: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

j: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16140 Å2
ΔGint	-72.6 kcal/mol
Surface area	16100 Å2
Method	PISA

10

V: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

W: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

X: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16000 Å2
ΔGint	-72 kcal/mol
Surface area	16190 Å2
Method	PISA

11

2: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

3: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

4: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16110 Å2
ΔGint	-73.2 kcal/mol
Surface area	16190 Å2
Method	PISA

12

5: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

6: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

7: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16130 Å2
ΔGint	-74.6 kcal/mol
Surface area	16110 Å2
Method	PISA

13

J: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

K: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

L: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16060 Å2
ΔGint	-72.2 kcal/mol
Surface area	16150 Å2
Method	PISA

14

G: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

H: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

I: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16060 Å2
ΔGint	-72.8 kcal/mol
Surface area	16120 Å2
Method	PISA

15

b: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

c: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

d: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16120 Å2
ΔGint	-74.4 kcal/mol
Surface area	16150 Å2
Method	PISA

16

M: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

N: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

O: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

hetero molecules

Summary:

• defined by software
• 50.6 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,581	12
Polymers	49,295	3
Non-polymers	1,285	9
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	16080 Å2
ΔGint	-72 kcal/mol
Surface area	16150 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	97.060, 97.070, 193.850
Angle α, β, γ (deg.)	89.72, 88.47, 90.11
Int Tables number	1
Space group name H-M	P1

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
17	1	Q
18	1	R
19	1	S
20	1	T
21	1	U
22	1	V
23	1	W
24	1	X
25	1	Y
26	1	Z
27	1	1
28	1	2
29	1	3
30	1	4
31	1	5
1	2	A
2	2	6
3	2	7
4	2	8
5	2	9
6	2	a
7	2	b
8	2	c
9	2	d
10	2	e
11	2	f
12	2	g
13	2	h
14	2	i
15	2	j
16	2	l
17	2	m

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	2 - 144
2	1	1	2	B	2 - 144
3	1	1	2	C	2 - 144
4	1	1	2	D	2 - 144
5	1	1	2	E	2 - 144
6	1	1	2	F	2 - 144
7	1	1	2	G	2 - 144
8	1	1	2	H	2 - 144
9	1	1	2	I	2 - 144
10	1	1	2	J	2 - 144
11	1	1	2	K	2 - 144
12	1	1	2	L	2 - 144
13	1	1	2	M	2 - 144
14	1	1	2	N	2 - 144
15	1	1	2	O	2 - 144
16	1	1	2	P	2 - 144
17	1	1	2	Q	2 - 144
18	1	1	2	R	2 - 144
19	1	1	2	S	2 - 144
20	1	1	2	T	2 - 144
21	1	1	2	U	2 - 144
22	1	1	2	V	2 - 144
23	1	1	2	W	2 - 144
24	1	1	2	X	2 - 144
25	1	1	2	Y	2 - 144
26	1	1	2	Z	2 - 144
27	1	1	2	1	2 - 144
28	1	1	2	2	2 - 144
29	1	1	2	3	2 - 144
30	1	1	2	4	2 - 144
31	1	1	2	5	2 - 144
1	1	2	2	A	2 - 144
2	1	2	2	6	2 - 144
3	1	2	2	7	2 - 144
4	1	2	2	8	2 - 144
5	1	2	2	9	2 - 144
6	1	2	2	a	2 - 144
7	1	2	2	b	2 - 144
8	1	2	2	c	2 - 144
9	1	2	2	d	2 - 144
10	1	2	2	e	2 - 144
11	1	2	2	f	2 - 144
12	1	2	2	g	2 - 144
13	1	2	2	h	2 - 144
14	1	2	2	i	2 - 144
15	1	2	2	j	2 - 144
16	1	2	2	l	2 - 144
17	1	2	2	m	2 - 144

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.119621, -0.10938, -0.986776), (-0.992818, -0.011425, -0.119088), (0.001752, 0.993934, -0.109961)	47.35937, 5.44887, 53.5096
3	given	(0.118398, -0.992947, 0.006148), (-0.109551, -0.006908, 0.993957), (-0.986905, -0.118356, -0.109597)	-0.53811, -47.97639, 53.22149
4	given	(0.993807, 0.008221, 0.110812), (0.11073, 0.009899, -0.993801), (-0.009267, 0.999917, 0.008927)	-2.81483, 2.25468, 50.46516
5	given	(0.008243, -0.006693, 0.999944), (-0.117604, 0.993031, 0.007616), (-0.993026, -0.11766, 0.007399)	-2.78775, 2.47906, 50.2273
6	given	(0.111799, -0.987344, 0.112484), (-0.986659, -0.12377, -0.105758), (0.118341, -0.09916, -0.988009)	-3.02989, 2.26764, 50.1998
7	given	(-0.014018, -0.9921, 0.12466), (0.112443, -0.125446, -0.985708), (0.993559, 0.0002, 0.113314)	0.11245, -0.69306, -0.11801
8	given	(-0.994501, -0.104159, 0.010937), (-0.104698, 0.986096, -0.129045), (0.002656, -0.12948, -0.991578)	47.57328, 5.36468, 52.83185
9	given	(-0.107758, 0.006482, 0.994156), (0.987933, 0.112597, 0.106349), (-0.111249, 0.99362, -0.018537)	0.19629, -48.09008, 53.36186
10	given	(-0.986555, -0.121789, -0.108976), (-0.122403, 0.108817, 0.986497), (-0.108286, 0.986573, -0.122261)	50.54827, -44.57251, 56.55306
11	given	(0.002528, -0.116755, -0.993158), (0.00495, 0.99315, -0.116742), (0.999985, -0.004621, 0.003089)	50.14241, 2.86305, 2.48774
12	given	(0.002616, -0.999989, -0.003937), (0.993238, 0.002142, 0.116078), (-0.116068, -0.004214, 0.993232)	2.64131, -51.16776, 3.32213
13	given	(0.099058, 0.009802, -0.995033), (0.011139, -0.9999, -0.008741), (-0.995019, -0.010218, -0.099157)	50.54804, -45.26357, 55.31411
14	given	(-0.003416, 0.994046, -0.108906), (-0.999949, -0.002355, 0.009863), (0.009548, 0.108934, 0.994003)	50.7015, 1.93252, 2.61079
15	given	(0.99275, 0.118509, -0.020055), (0.020153, 0.00037, 0.999797), (0.118493, -0.992953, -0.002021)	3.66579, -50.86861, 2.68448
16	given	(-0.002513, 0.999895, 0.014289), (-0.002014, 0.014284, -0.999896), (-0.999995, -0.002541, 0.001978)	47.70943, 5.86269, 53.12786
17	given	(0.986842, 0.118855, 0.10962), (0.120176, -0.992737, -0.005497), (0.10817, 0.018599, -0.993958)	-0.08332, -48.30709, 53.65716
18	given	(-0.003333, 0.108181, 0.994126), (-0.993254, -0.115591, 0.009249), (0.115913, -0.987388, 0.107836)	-0.18815, -0.60905, -0.35909
19	given	(-0.992902, -0.002972, -0.118896), (-0.01132, -0.992788, 0.119351), (-0.118393, 0.11985, 0.985707)	53.88813, -48.49456, 6.57125
20	given	(-0.000893, -0.010027, -0.999949), (0.999999, -0.001162, -0.000881), (-0.001153, -0.999949, 0.010028)	52.62896, -48.28378, 4.76398
21	given	(-0.107556, 0.986219, -0.125714), (-0.007877, 0.125598, 0.99205), (0.994168, 0.107692, -0.00574)	54.00499, -47.08855, 5.14778
22	given	(-0.999972, -0.004511, 0.005926), (-0.005418, -0.105196, -0.994437), (0.005109, -0.994441, 0.105169)	50.32329, 2.84167, 1.93657
23	given	(-0.109068, 0.098076, 0.989184), (0.11514, -0.987176, 0.110572), (0.987343, 0.125955, 0.096377)	2.3992, -51.58133, 3.03294
24	given	(-0.124461, 0.992171, 0.010306), (0.992089, 0.124609, -0.015207), (-0.016372, 0.008332, -0.999831)	51.125, -44.68394, 56.80988
25	given	(0.117628, -0.121821, 0.985557), (0.008612, 0.992535, 0.121656), (-0.99302, -0.005822, 0.117799)	86.3856, -45.74787, 124.57925
26	given	(0.00416, -0.999988, -0.002572), (-0.999968, -0.004177, 0.0068), (-0.006811, 0.002543, -0.999974)	55.61415, 66.88711, -40.27971
27	given	(0.993127, -0.116021, -0.015451), (-0.002087, 0.114441, -0.993428), (0.117026, 0.986632, 0.113412)	-60.71336, -94.56725, -5.08862
28	given	(-0.005466, -0.001695, -0.999984), (-0.992874, 0.119052, 0.005226), (0.119042, 0.992887, -0.002334)	-42.79777, 62.06437, -13.37552
29	given	(0.985886, -0.111564, -0.124826), (0.125338, 0.986158, 0.108548), (0.110988, -0.122662, 0.986223)	-67.41544, -56.8929, 89.58202
30	given	(-0.010069, -0.992688, -0.120287), (0.005879, -0.12035, 0.992714), (-0.999932, 0.009288, 0.007048)	48.58635, 48.7104, 116.71264
31	given	(0.123786, -0.010897, 0.992249), (-0.992301, 0.002645, 0.123821), (-0.003974, -0.999937, -0.010486)	82.71183, 73.98061, 58.12456

Components

Protein , 1 types, 48 molecules 1 2 3 4 5 6 7 8 9 A B C D E F G H I J K L M N O P Q R S T U ...

#1: Protein

1 2 3 4 5 6 7 8 9 A B C D E F G H I J ...
PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF / DUTPASE / DUTP PYROPHOSPHATASE

Details:

Mass: 16431.760 Da / Num. of mol.: 48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O31801, dUTP diphosphatase

Non-polymers , 5 types, 4872 molecules

#2: Chemical

1-1145 2-1145 3-1145 4-1145 5-1145 6-1145 7-1145 8-1145 9-1145 A-1145 B-1145 C-1145 D-1145 E-1145 F-1145 G-1145 H-1145 I-1145 J-1145 K-1145 ...
ChemComp-DUR / 2'-DEOXYURIDINE / Deoxyuridine

Details:

Mass: 228.202 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C₉H₁₂N₂O₅ / Comment: antivirus*YM

#3: Chemical

1-1146 2-1146 3-1146 4-1146 5-1146 6-1146 7-1146 8-1146 9-1146 A-1146 B-1146 C-1146 D-1146 E-1146 F-1146 G-1146 H-1146 I-1146 J-1146 K-1146 ...
ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate

Details:

Mass: 175.959 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: H₂O₇P₂

#4: Chemical

1-1147 2-1147 3-1147 4-1147 5-1147 6-1147 7-1147 8-1147 9-1147 A-1147 B-1147 C-1147 D-1147 E-1147 F-1147 G-1147 H-1147 I-1147 J-1147 K-1147 ...
ChemComp-MG / MAGNESIUM ION

Details:

Mass: 24.305 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Mg

#5: Chemical

e-1148 l-1148 ChemComp-PO4 / PHOSPHATE ION / Phosphate

Details:

Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄

#6: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 4726 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.32 ų/Da / Density % sol: 47 % / Description: NONE
• Crystal grow: pH: 4.6 / Details: 30% MPD, 0.1 M SODIUM ACETATE PH 4.6, 0.02 M CACL2

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9704
• Detector: Type: ADSC CCD / Detector: CCD / Date: Feb 19, 2011
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9704 Å / Relative weight: 1
• Reflection: Resolution: 2.01→36.44 Å / Num. obs: 434755 / % possible obs: 96.7 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / R_merge(I) obs: 0.09 / Net I/σ(I): 5.9
• Reflection shell: Resolution: 2.01→2.06 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 2.4 / % possible all: 95.9

Processing

Software

Name	Version	Classification
REFMAC	5.6.0119	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XCD

2xcd

Resolution: 2.01→36.44 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.935 / SU B: 4.141 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.21185	22967	5 %	RANDOM
Rwork	0.16909	-	-	-
obs	0.17122	434755	96.74 %	-

• 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 mean: 22.493 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.36 Å2	-0.3 Å2	0.01 Å2
2-	-	-0.65 Å2	0.32 Å2
3-	-	-	1 Å2

Refinement step

Cycle: LAST / Resolution: 2.01→36.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	54570	0	1258	4726	60554

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.02	57160
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	39715
X-RAY DIFFRACTION	r_angle_refined_deg	1.902	1.988	77133
X-RAY DIFFRACTION	r_angle_other_deg	1.31	3	96931
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.438	5	6902
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.691	24.631	2628
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.992	15	10586
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.815	15	338
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	8308
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	62088
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	11302
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1006	medium positional	0.05	0.5
1	2	B	1006	medium positional	0.07	0.5
1	3	C	1006	medium positional	0.06	0.5
1	4	D	1006	medium positional	0.11	0.5
1	5	E	1006	medium positional	0.07	0.5
1	6	F	1006	medium positional	0.08	0.5
1	7	G	1006	medium positional	0.06	0.5
1	8	H	1006	medium positional	0.07	0.5
1	9	I	1006	medium positional	0.1	0.5
1	10	J	1006	medium positional	0.06	0.5
1	11	K	1006	medium positional	0.06	0.5
1	12	L	1006	medium positional	0.06	0.5
1	13	M	1006	medium positional	0.06	0.5
1	14	N	1006	medium positional	0.06	0.5
1	15	O	1006	medium positional	0.06	0.5
1	16	P	1006	medium positional	0.07	0.5
1	17	Q	1006	medium positional	0.06	0.5
1	18	R	1006	medium positional	0.06	0.5
1	19	S	1006	medium positional	0.09	0.5
1	20	T	1006	medium positional	0.06	0.5
1	21	U	1006	medium positional	0.06	0.5
1	22	V	1006	medium positional	0.09	0.5
1	23	W	1006	medium positional	0.06	0.5
1	24	X	1006	medium positional	0.06	0.5
1	25	Y	1006	medium positional	0.06	0.5
1	26	Z	1006	medium positional	0.06	0.5
1	27	1	1006	medium positional	0.1	0.5
1	28	2	1006	medium positional	0.14	0.5
1	29	3	1006	medium positional	0.12	0.5
1	30	4	1006	medium positional	0.14	0.5
1	31	5	1006	medium positional	0.1	0.5
2	1	A	1030	medium positional	0.06	0.5
2	2	6	1030	medium positional	0.11	0.5
2	3	7	1030	medium positional	0.09	0.5
2	4	8	1030	medium positional	0.15	0.5
2	5	9	1030	medium positional	0.09	0.5
2	6	a	1030	medium positional	0.06	0.5
2	7	b	1030	medium positional	0.05	0.5
2	8	c	1030	medium positional	0.05	0.5
2	9	d	1030	medium positional	0.05	0.5
2	10	e	1030	medium positional	0.06	0.5
2	11	f	1030	medium positional	0.06	0.5
2	12	g	1030	medium positional	0.06	0.5
2	13	h	1030	medium positional	0.06	0.5
2	14	i	1030	medium positional	0.06	0.5
2	15	j	1030	medium positional	0.05	0.5
2	16	l	1030	medium positional	0.05	0.5
2	17	m	1030	medium positional	0.05	0.5
1	1	A	818	tight thermal	4	0.5
1	2	B	818	tight thermal	3.1	0.5
1	3	C	818	tight thermal	4.43	0.5
1	4	D	818	tight thermal	3.01	0.5
1	5	E	818	tight thermal	2.22	0.5
1	6	F	818	tight thermal	2.99	0.5
1	7	G	818	tight thermal	3.59	0.5
1	8	H	818	tight thermal	3.43	0.5
1	9	I	818	tight thermal	3.29	0.5
1	10	J	818	tight thermal	1.92	0.5
1	11	K	818	tight thermal	2.55	0.5
1	12	L	818	tight thermal	1.89	0.5
1	13	M	818	tight thermal	2.11	0.5
1	14	N	818	tight thermal	2.92	0.5
1	15	O	818	tight thermal	2.65	0.5
1	16	P	818	tight thermal	3.44	0.5
1	17	Q	818	tight thermal	2.01	0.5
1	18	R	818	tight thermal	2.15	0.5
1	19	S	818	tight thermal	2.16	0.5
1	20	T	818	tight thermal	2.5	0.5
1	21	U	818	tight thermal	1.9	0.5
1	22	V	818	tight thermal	2.07	0.5
1	23	W	818	tight thermal	2.11	0.5
1	24	X	818	tight thermal	2.44	0.5
1	25	Y	818	tight thermal	3.07	0.5
1	26	Z	818	tight thermal	4.07	0.5
1	27	1	818	tight thermal	3.32	0.5
1	28	2	818	tight thermal	2.18	0.5
1	29	3	818	tight thermal	3.18	0.5
1	30	4	818	tight thermal	3.21	0.5
1	31	5	818	tight thermal	5.11	0.5
2	1	A	818	tight thermal	2.95	0.5
2	2	6	818	tight thermal	3.52	0.5
2	3	7	818	tight thermal	3.83	0.5
2	4	8	818	tight thermal	4.46	0.5
2	5	9	818	tight thermal	3.12	0.5
2	6	a	818	tight thermal	4.16	0.5
2	7	b	818	tight thermal	2.22	0.5
2	8	c	818	tight thermal	2.29	0.5
2	9	d	818	tight thermal	2.57	0.5
2	10	e	818	tight thermal	2.23	0.5
2	11	f	818	tight thermal	2.64	0.5
2	12	g	818	tight thermal	2.55	0.5
2	13	h	818	tight thermal	3.41	0.5
2	14	i	818	tight thermal	4.32	0.5
2	15	j	818	tight thermal	2.55	0.5
2	16	l	818	tight thermal	5.66	0.5
2	17	m	818	tight thermal	4.56	0.5
1	1	A	1006	medium thermal	4.4	2
1	2	B	1006	medium thermal	3.83	2
1	3	C	1006	medium thermal	4.14	2
1	4	D	1006	medium thermal	3.71	2
1	5	E	1006	medium thermal	2.69	2
1	6	F	1006	medium thermal	3.38	2
1	7	G	1006	medium thermal	3.99	2
1	8	H	1006	medium thermal	3.93	2
1	9	I	1006	medium thermal	4.01	2
1	10	J	1006	medium thermal	2.82	2
1	11	K	1006	medium thermal	3.16	2
1	12	L	1006	medium thermal	2.54	2
1	13	M	1006	medium thermal	2.92	2
1	14	N	1006	medium thermal	3.51	2
1	15	O	1006	medium thermal	3	2
1	16	P	1006	medium thermal	4	2
1	17	Q	1006	medium thermal	2.37	2
1	18	R	1006	medium thermal	2.85	2
1	19	S	1006	medium thermal	2.48	2
1	20	T	1006	medium thermal	3.54	2
1	21	U	1006	medium thermal	2.49	2
1	22	V	1006	medium thermal	2.8	2
1	23	W	1006	medium thermal	2.86	2
1	24	X	1006	medium thermal	3.11	2
1	25	Y	1006	medium thermal	3.53	2
1	26	Z	1006	medium thermal	4.23	2
1	27	1	1006	medium thermal	3.59	2
1	28	2	1006	medium thermal	2.73	2
1	29	3	1006	medium thermal	3.35	2
1	30	4	1006	medium thermal	3.51	2
1	31	5	1006	medium thermal	5.47	2
2	1	A	1030	medium thermal	3.48	2
2	2	6	1030	medium thermal	3.97	2
2	3	7	1030	medium thermal	4.5	2
2	4	8	1030	medium thermal	4.72	2
2	5	9	1030	medium thermal	3.94	2
2	6	a	1030	medium thermal	4.78	2
2	7	b	1030	medium thermal	2.8	2
2	8	c	1030	medium thermal	2.85	2
2	9	d	1030	medium thermal	2.98	2
2	10	e	1030	medium thermal	2.81	2
2	11	f	1030	medium thermal	3.35	2
2	12	g	1030	medium thermal	3.06	2
2	13	h	1030	medium thermal	3.9	2
2	14	i	1030	medium thermal	4.79	2
2	15	j	1030	medium thermal	3.16	2
2	16	l	1030	medium thermal	5.68	2
2	17	m	1030	medium thermal	4.74	2

LS refinement shell

Resolution: 2.007→2.059 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.291	1671	-
Rwork	0.239	31851	-
obs	-	-	95.82 %