PDB-6huf: Coping with strong translational non-crystallographic symmetry an...

Basic information

• Entry: Database: PDB / ID: 6huf
• Title: Coping with strong translational non-crystallographic symmetry and extreme anisotropy in molecular replacement with Phaser: human Rab27a
• Components: Ras-related protein Rab-27A
• Keywords: EXOCYTOSIS / GTPase / Vesicle transport

Function / homology

Function:

multivesicular body organization / cytotoxic T cell degranulation / positive regulation of constitutive secretory pathway / positive regulation of regulated secretory pathway / melanosome localization / natural killer cell degranulation / exosomal secretion / melanosome transport / Weibel-Palade body / exocytic vesicle / melanocyte differentiation / melanosome membrane / multivesicular body sorting pathway / RAB geranylgeranylation / myosin V binding / multivesicular body membrane / RAB GEFs exchange GTP for GDP on RABs / complement-dependent cytotoxicity / positive regulation of reactive oxygen species biosynthetic process / synaptic vesicle transport / Insulin processing / exocytosis / positive regulation of exocytosis / antigen processing and presentation / protein secretion / photoreceptor outer segment / positive regulation of phagocytosis / small monomeric GTPase / G protein activity / secretory granule / specific granule lumen / GDP binding / blood coagulation / melanosome / late endosome / lysosome / apical plasma membrane / protein domain specific binding / GTPase activity / dendrite / Neutrophil degranulation / positive regulation of gene expression / GTP binding / Golgi apparatus / extracellular exosome / extracellular region / cytosol

Domain/homology:

Rab27a/b / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-27A

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
• Authors: Jamshidiha, M. / Perez-Dorado, I. / Murray, J.W. / Tate, E.W. / Cota, E. / Read, R.J.

Funding support

United Kingdom, 2items

Organization	Grant number	Country
Wellcome Trust	082961/Z/07/Z	United Kingdom
Cancer Research UK	C29637/A20781	United Kingdom

• Citation: Journal: Acta Crystallogr D Struct Biol / Year: 2019; Title: Coping with strong translational noncrystallographic symmetry and extreme anisotropy in molecular replacement with Phaser: human Rab27a.; Authors: Jamshidiha, M. / Perez-Dorado, I. / Murray, J.W. / Tate, E.W. / Cota, E. / Read, R.J.

History

Deposition	Oct 8, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2019	Group: Data collection / Database references / Category: citation / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jul 10, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Jan 24, 2024	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.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

Assembly

Deposited unit

A: Ras-related protein Rab-27A

O: Ras-related protein Rab-27A

N: Ras-related protein Rab-27A

B: Ras-related protein Rab-27A

E: Ras-related protein Rab-27A

C: Ras-related protein Rab-27A

K: Ras-related protein Rab-27A

M: Ras-related protein Rab-27A

D: Ras-related protein Rab-27A

P: Ras-related protein Rab-27A

F: Ras-related protein Rab-27A

J: Ras-related protein Rab-27A

G: Ras-related protein Rab-27A

I: Ras-related protein Rab-27A

H: Ras-related protein Rab-27A

L: Ras-related protein Rab-27A

hetero molecules

Summary:

• 341 kDa, 16 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	340,926	48
Polymers	332,182	16
Non-polymers	8,744	32
Water	108	6

1

A: Ras-related protein Rab-27A

B: Ras-related protein Rab-27A

C: Ras-related protein Rab-27A

D: Ras-related protein Rab-27A

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration, The protein runs as a monomeric protein in a gel filtration column.
• 85.2 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	85,232	12
Polymers	83,046	4
Non-polymers	2,186	8
Water	18	1

Symmetry operations:

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

2

O: Ras-related protein Rab-27A

N: Ras-related protein Rab-27A

M: Ras-related protein Rab-27A

P: Ras-related protein Rab-27A

hetero molecules

Summary:

• defined by author
• 85.2 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	85,232	12
Polymers	83,046	4
Non-polymers	2,186	8
Water	0

Symmetry operations:

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

3

E: Ras-related protein Rab-27A

F: Ras-related protein Rab-27A

G: Ras-related protein Rab-27A

H: Ras-related protein Rab-27A

hetero molecules

Summary:

• defined by author
• 85.2 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	85,232	12
Polymers	83,046	4
Non-polymers	2,186	8
Water	18	1

Symmetry operations:

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

4

K: Ras-related protein Rab-27A

J: Ras-related protein Rab-27A

I: Ras-related protein Rab-27A

L: Ras-related protein Rab-27A

hetero molecules

Summary:

• defined by author
• 85.2 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	85,232	12
Polymers	83,046	4
Non-polymers	2,186	8
Water	0

Symmetry operations:

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

Unit cell

Length a, b, c (Å)	130.420, 132.410, 230.590
Angle α, β, γ (deg.)	90.00, 103.57, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	O
1	2	A
2	2	N
1	3	A
2	3	B
1	4	A
2	4	E
1	5	A
2	5	C
1	6	A
2	6	K
1	7	A
2	7	M
1	8	A
2	8	D
1	9	A
2	9	P
1	10	A
2	10	F
1	11	A
2	11	J
1	12	A
2	12	G
1	13	A
2	13	I
1	14	A
2	14	H
1	15	A
2	15	L
1	16	O
2	16	N
1	17	O
2	17	B
1	18	O
2	18	E
1	19	O
2	19	C
1	20	O
2	20	K
1	21	O
2	21	M
1	22	O
2	22	D
1	23	O
2	23	P
1	24	O
2	24	F
1	25	O
2	25	J
1	26	O
2	26	G
1	27	O
2	27	I
1	28	O
2	28	H
1	29	O
2	29	L
1	30	N
2	30	B
1	31	N
2	31	E
1	32	N
2	32	C
1	33	N
2	33	K
1	34	N
2	34	M
1	35	N
2	35	D
1	36	N
2	36	P
1	37	N
2	37	F
1	38	N
2	38	J
1	39	N
2	39	G
1	40	N
2	40	I
1	41	N
2	41	H
1	42	N
2	42	L
1	43	B
2	43	E
1	44	B
2	44	C
1	45	B
2	45	K
1	46	B
2	46	M
1	47	B
2	47	D
1	48	B
2	48	P
1	49	B
2	49	F
1	50	B
2	50	J
1	51	B
2	51	G
1	52	B
2	52	I
1	53	B
2	53	H
1	54	B
2	54	L
1	55	E
2	55	C
1	56	E
2	56	K
1	57	E
2	57	M
1	58	E
2	58	D
1	59	E
2	59	P
1	60	E
2	60	F
1	61	E
2	61	J
1	62	E
2	62	G
1	63	E
2	63	I
1	64	E
2	64	H
1	65	E
2	65	L
1	66	C
2	66	K
1	67	C
2	67	M
1	68	C
2	68	D
1	69	C
2	69	P
1	70	C
2	70	F
1	71	C
2	71	J
1	72	C
2	72	G
1	73	C
2	73	I
1	74	C
2	74	H
1	75	C
2	75	L
1	76	K
2	76	M
1	77	K
2	77	D
1	78	K
2	78	P
1	79	K
2	79	F
1	80	K
2	80	J
1	81	K
2	81	G
1	82	K
2	82	I
1	83	K
2	83	H
1	84	K
2	84	L
1	85	M
2	85	D
1	86	M
2	86	P
1	87	M
2	87	F
1	88	M
2	88	J
1	89	M
2	89	G
1	90	M
2	90	I
1	91	M
2	91	H
1	92	M
2	92	L
1	93	D
2	93	P
1	94	D
2	94	F
1	95	D
2	95	J
1	96	D
2	96	G
1	97	D
2	97	I
1	98	D
2	98	H
1	99	D
2	99	L
1	100	P
2	100	F
1	101	P
2	101	J
1	102	P
2	102	G
1	103	P
2	103	I
1	104	P
2	104	H
1	105	P
2	105	L
1	106	F
2	106	J
1	107	F
2	107	G
1	108	F
2	108	I
1	109	F
2	109	H
1	110	F
2	110	L
1	111	J
2	111	G
1	112	J
2	112	I
1	113	J
2	113	H
1	114	J
2	114	L
1	115	G
2	115	I
1	116	G
2	116	H
1	117	G
2	117	L
1	118	I
2	118	H
1	119	I
2	119	L
1	120	H
2	120	L

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 8 - 178 / Label seq-ID: 8 - 178

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	O	B
1	2	A	A
2	2	N	C
1	3	A	A
2	3	B	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	C	F
1	6	A	A
2	6	K	G
1	7	A	A
2	7	M	H
1	8	A	A
2	8	D	I
1	9	A	A
2	9	P	J
1	10	A	A
2	10	F	K
1	11	A	A
2	11	J	L
1	12	A	A
2	12	G	M
1	13	A	A
2	13	I	N
1	14	A	A
2	14	H	O
1	15	A	A
2	15	L	P
1	16	O	B
2	16	N	C
1	17	O	B
2	17	B	D
1	18	O	B
2	18	E	E
1	19	O	B
2	19	C	F
1	20	O	B
2	20	K	G
1	21	O	B
2	21	M	H
1	22	O	B
2	22	D	I
1	23	O	B
2	23	P	J
1	24	O	B
2	24	F	K
1	25	O	B
2	25	J	L
1	26	O	B
2	26	G	M
1	27	O	B
2	27	I	N
1	28	O	B
2	28	H	O
1	29	O	B
2	29	L	P
1	30	N	C
2	30	B	D
1	31	N	C
2	31	E	E
1	32	N	C
2	32	C	F
1	33	N	C
2	33	K	G
1	34	N	C
2	34	M	H
1	35	N	C
2	35	D	I
1	36	N	C
2	36	P	J
1	37	N	C
2	37	F	K
1	38	N	C
2	38	J	L
1	39	N	C
2	39	G	M
1	40	N	C
2	40	I	N
1	41	N	C
2	41	H	O
1	42	N	C
2	42	L	P
1	43	B	D
2	43	E	E
1	44	B	D
2	44	C	F
1	45	B	D
2	45	K	G
1	46	B	D
2	46	M	H
1	47	B	D
2	47	D	I
1	48	B	D
2	48	P	J
1	49	B	D
2	49	F	K
1	50	B	D
2	50	J	L
1	51	B	D
2	51	G	M
1	52	B	D
2	52	I	N
1	53	B	D
2	53	H	O
1	54	B	D
2	54	L	P
1	55	E	E
2	55	C	F
1	56	E	E
2	56	K	G
1	57	E	E
2	57	M	H
1	58	E	E
2	58	D	I
1	59	E	E
2	59	P	J
1	60	E	E
2	60	F	K
1	61	E	E
2	61	J	L
1	62	E	E
2	62	G	M
1	63	E	E
2	63	I	N
1	64	E	E
2	64	H	O
1	65	E	E
2	65	L	P
1	66	C	F
2	66	K	G
1	67	C	F
2	67	M	H
1	68	C	F
2	68	D	I
1	69	C	F
2	69	P	J
1	70	C	F
2	70	F	K
1	71	C	F
2	71	J	L
1	72	C	F
2	72	G	M
1	73	C	F
2	73	I	N
1	74	C	F
2	74	H	O
1	75	C	F
2	75	L	P
1	76	K	G
2	76	M	H
1	77	K	G
2	77	D	I
1	78	K	G
2	78	P	J
1	79	K	G
2	79	F	K
1	80	K	G
2	80	J	L
1	81	K	G
2	81	G	M
1	82	K	G
2	82	I	N
1	83	K	G
2	83	H	O
1	84	K	G
2	84	L	P
1	85	M	H
2	85	D	I
1	86	M	H
2	86	P	J
1	87	M	H
2	87	F	K
1	88	M	H
2	88	J	L
1	89	M	H
2	89	G	M
1	90	M	H
2	90	I	N
1	91	M	H
2	91	H	O
1	92	M	H
2	92	L	P
1	93	D	I
2	93	P	J
1	94	D	I
2	94	F	K
1	95	D	I
2	95	J	L
1	96	D	I
2	96	G	M
1	97	D	I
2	97	I	N
1	98	D	I
2	98	H	O
1	99	D	I
2	99	L	P
1	100	P	J
2	100	F	K
1	101	P	J
2	101	J	L
1	102	P	J
2	102	G	M
1	103	P	J
2	103	I	N
1	104	P	J
2	104	H	O
1	105	P	J
2	105	L	P
1	106	F	K
2	106	J	L
1	107	F	K
2	107	G	M
1	108	F	K
2	108	I	N
1	109	F	K
2	109	H	O
1	110	F	K
2	110	L	P
1	111	J	L
2	111	G	M
1	112	J	L
2	112	I	N
1	113	J	L
2	113	H	O
1	114	J	L
2	114	L	P
1	115	G	M
2	115	I	N
1	116	G	M
2	116	H	O
1	117	G	M
2	117	L	P
1	118	I	N
2	118	H	O
1	119	I	N
2	119	L	P
1	120	H	O
2	120	L	P

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120

Components

#1: Protein

A O N B E C K M D P F J G I H L
Ras-related protein Rab-27A / Rab-27 / GTP-binding protein Ram

Details:

Mass: 20761.395 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Details: This is a mutant variant of Rab27a, designed to enhance crystallisation properties of Rab27a
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB27A, RAB27 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P51159

#2: Chemical

A-201 O-201 N-201 B-201 E-201 C-201 K-201 M-201 D-201 P-201 F-201 J-201 G-201 I-201 H-201 L-201
ChemComp-MG / MAGNESIUM ION

Details:

Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg

#3: Chemical

A-202 O-202 N-202 B-202 E-202 C-202 K-202 M-202 D-202 P-202 F-202 J-202 G-202 I-202 H-202 L-202
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

Details:

Mass: 522.196 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₃P₃
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

#4: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.99 ų/Da / Density % sol: 58.84 % / Description: Cubic crystals
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 ; Details: 20% (v/v) ethylene glycol, 10% (w/v) PEG 8000, 30 mM MgCl2, 30 mM CaCl2 and 100 mM HEPES pH 7.5; PH range: 7-8

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
• Detector: Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2016
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97949 Å / Relative weight: 1
• Reflection: Resolution: 2.82→80.15 Å / Num. obs: 91204 / % possible obs: 99.9 % / Redundancy: 3.7 % / B_iso Wilson estimate: 114.3 Ų / CC_1/2: 0.995 / R_merge(I) obs: 0.081 / R_pim(I) all: 0.073 / R_rim(I) all: 0.109 / Net I/σ(I): 7.9
• Reflection shell: Resolution: 2.82→2.88 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.991 / Mean I/σ(I) obs: 1 / Num. unique obs: 4512 / CC_1/2: 0.688 / R_pim(I) all: 0.691 / R_rim(I) all: 1.038 / % possible all: 100

Processing

Software

Name	Version	Classification
REFMAC	5.8.0189	refinement
DIALS		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BC1

3bc1

Resolution: 2.82→80.15 Å / Cor.coef. F_o:F_c: 0.895 / Cor.coef. F_o:F_c free: 0.87 / SU B: 30.807 / SU ML: 0.593 / Cross valid method: THROUGHOUT / ESU R Free: 0.577 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.34236	3513	5 %	RANDOM
Rwork	0.31185	-	-	-
obs	0.31339	66055	75.8 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 67.995 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	7.15 Å2	0 Å2	-19.74 Å2
2-	-	-6.81 Å2	0 Å2
3-	-	-	8.23 Å2

Refinement step

Cycle: 1 / Resolution: 2.82→80.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18443	0	528	6	18977

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	19264
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	15461
X-RAY DIFFRACTION	r_angle_refined_deg	1.479	1.648	26499
X-RAY DIFFRACTION	r_angle_other_deg	1.366	1.583	35038
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.213	5	2720
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.041	23.032	696
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.487	15	2150
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.003	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	2912
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	22863
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4089
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	7.408	8.413	10928
X-RAY DIFFRACTION	r_mcbond_other	7.407	8.412	10927
X-RAY DIFFRACTION	r_mcangle_it	11.548	12.607	13632
X-RAY DIFFRACTION	r_mcangle_other	11.548	12.608	13633
X-RAY DIFFRACTION	r_scbond_it	6.693	8.257	8336
X-RAY DIFFRACTION	r_scbond_other	6.694	8.258	8334
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	10.278	12.295	12868
X-RAY DIFFRACTION	r_long_range_B_refined	15.399	100.84	21158
X-RAY DIFFRACTION	r_long_range_B_other	15.399	100.837	21159
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	4527	0
1	2	O	4527	0
2	1	A	4499	0
2	2	N	4499	0
3	1	A	4504	0.01
3	2	B	4504	0.01
4	1	A	4501	0.01
4	2	E	4501	0.01
5	1	A	4504	0
5	2	C	4504	0
6	1	A	4531	0.01
6	2	K	4531	0.01
7	1	A	4506	0
7	2	M	4506	0
8	1	A	4507	0
8	2	D	4507	0
9	1	A	4477	0.03
9	2	P	4477	0.03
10	1	A	4505	0
10	2	F	4505	0
11	1	A	4501	0.02
11	2	J	4501	0.02
12	1	A	4503	0
12	2	G	4503	0
13	1	A	4502	0
13	2	I	4502	0
14	1	A	4504	0
14	2	H	4504	0
15	1	A	4502	0
15	2	L	4502	0
16	1	O	4493	0.01
16	2	N	4493	0.01
17	1	O	4502	0.01
17	2	B	4502	0.01
18	1	O	4500	0.01
18	2	E	4500	0.01
19	1	O	4501	0.01
19	2	C	4501	0.01
20	1	O	4503	0.01
20	2	K	4503	0.01
21	1	O	4499	0.01
21	2	M	4499	0.01
22	1	O	4500	0.01
22	2	D	4500	0.01
23	1	O	4473	0.03
23	2	P	4473	0.03
24	1	O	4502	0.01
24	2	F	4502	0.01
25	1	O	4496	0.02
25	2	J	4496	0.02
26	1	O	4497	0.01
26	2	G	4497	0.01
27	1	O	4497	0.01
27	2	I	4497	0.01
28	1	O	4498	0.01
28	2	H	4498	0.01
29	1	O	4502	0.01
29	2	L	4502	0.01
30	1	N	4502	0
30	2	B	4502	0
31	1	N	4493	0
31	2	E	4493	0
32	1	N	4493	0
32	2	C	4493	0
33	1	N	4498	0.01
33	2	K	4498	0.01
34	1	N	4494	0
34	2	M	4494	0
35	1	N	4496	0
35	2	D	4496	0
36	1	N	4470	0.03
36	2	P	4470	0.03
37	1	N	4498	0
37	2	F	4498	0
38	1	N	4494	0.02
38	2	J	4494	0.02
39	1	N	4496	0
39	2	G	4496	0
40	1	N	4495	0
40	2	I	4495	0
41	1	N	4494	0
41	2	H	4494	0
42	1	N	4494	0
42	2	L	4494	0
43	1	B	4500	0
43	2	E	4500	0
44	1	B	4499	0
44	2	C	4499	0
45	1	B	4507	0.01
45	2	K	4507	0.01
46	1	B	4500	0
46	2	M	4500	0
47	1	B	4501	0
47	2	D	4501	0
48	1	B	4476	0.03
48	2	P	4476	0.03
49	1	B	4503	0
49	2	F	4503	0
50	1	B	4502	0.02
50	2	J	4502	0.02
51	1	B	4501	0
51	2	G	4501	0
52	1	B	4499	0
52	2	I	4499	0
53	1	B	4499	0
53	2	H	4499	0
54	1	B	4498	0
54	2	L	4498	0
55	1	E	4496	0
55	2	C	4496	0
56	1	E	4506	0
56	2	K	4506	0
57	1	E	4500	0
57	2	M	4500	0
58	1	E	4499	0
58	2	D	4499	0
59	1	E	4474	0.03
59	2	P	4474	0.03
60	1	E	4499	0
60	2	F	4499	0
61	1	E	4498	0.02
61	2	J	4498	0.02
62	1	E	4497	0.01
62	2	G	4497	0.01
63	1	E	4496	0
63	2	I	4496	0
64	1	E	4498	0
64	2	H	4498	0
65	1	E	4500	0
65	2	L	4500	0
66	1	C	4497	0.01
66	2	K	4497	0.01
67	1	C	4501	0
67	2	M	4501	0
68	1	C	4499	0
68	2	D	4499	0
69	1	C	4473	0.03
69	2	P	4473	0.03
70	1	C	4500	0
70	2	F	4500	0
71	1	C	4495	0.02
71	2	J	4495	0.02
72	1	C	4496	0
72	2	G	4496	0
73	1	C	4494	0
73	2	I	4494	0
74	1	C	4497	0
74	2	H	4497	0
75	1	C	4496	0
75	2	L	4496	0
76	1	K	4501	0
76	2	M	4501	0
77	1	K	4502	0.01
77	2	D	4502	0.01
78	1	K	4501	0.03
78	2	P	4501	0.03
79	1	K	4503	0
79	2	F	4503	0
80	1	K	4500	0.02
80	2	J	4500	0.02
81	1	K	4500	0
81	2	G	4500	0
82	1	K	4498	0.01
82	2	I	4498	0.01
83	1	K	4501	0
83	2	H	4501	0
84	1	K	4500	0
84	2	L	4500	0
85	1	M	4500	0
85	2	D	4500	0
86	1	M	4474	0.03
86	2	P	4474	0.03
87	1	M	4500	0
87	2	F	4500	0
88	1	M	4497	0.02
88	2	J	4497	0.02
89	1	M	4500	0
89	2	G	4500	0
90	1	M	4499	0
90	2	I	4499	0
91	1	M	4500	0
91	2	H	4500	0
92	1	M	4499	0
92	2	L	4499	0
93	1	D	4476	0.03
93	2	P	4476	0.03
94	1	D	4523	0.01
94	2	F	4523	0.01
95	1	D	4522	0.02
95	2	J	4522	0.02
96	1	D	4496	0
96	2	G	4496	0
97	1	D	4497	0
97	2	I	4497	0
98	1	D	4502	0
98	2	H	4502	0
99	1	D	4498	0
99	2	L	4498	0
100	1	P	4475	0.03
100	2	F	4475	0.03
101	1	P	4473	0.04
101	2	J	4473	0.04
102	1	P	4470	0.03
102	2	G	4470	0.03
103	1	P	4470	0.03
103	2	I	4470	0.03
104	1	P	4474	0.03
104	2	H	4474	0.03
105	1	P	4471	0.03
105	2	L	4471	0.03
106	1	F	4527	0.02
106	2	J	4527	0.02
107	1	F	4497	0
107	2	G	4497	0
108	1	F	4498	0
108	2	I	4498	0
109	1	F	4499	0
109	2	H	4499	0
110	1	F	4501	0
110	2	L	4501	0
111	1	J	4495	0.02
111	2	G	4495	0.02
112	1	J	4494	0.02
112	2	I	4494	0.02
113	1	J	4497	0.02
113	2	H	4497	0.02
114	1	J	4498	0.02
114	2	L	4498	0.02
115	1	G	4496	0
115	2	I	4496	0
116	1	G	4500	0
116	2	H	4500	0
117	1	G	4496	0
117	2	L	4496	0
118	1	I	4499	0
118	2	H	4499	0
119	1	I	4499	0
119	2	L	4499	0
120	1	H	4501	0
120	2	L	4501	0

LS refinement shell

Resolution: 2.82→2.893 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.49	170	-
Rwork	0.465	2950	-
obs	-	-	46.34 %