PDB-4rau: crystal structure of RTOFab in complex with human PF4

Basic information

• Entry: Database: PDB / ID: 4rau
• Title: crystal structure of RTOFab in complex with human PF4

Components

• Platelet factor 4
• RTOFab heavy chain
• RTOFab light chain

• Keywords: IMMUNE SYSTEM / RTO / PF4 / HIT / immunoglobulin / CXC chemokine / antibody / antigen / blood

Function / homology

Function:

CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / negative regulation of MHC class II biosynthetic process / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / killing by host of symbiont cells / chemokine-mediated signaling pathway / leukocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / defense response to protozoan / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of megakaryocyte differentiation / Common Pathway of Fibrin Clot Formation / negative regulation of angiogenesis / neutrophil chemotaxis / platelet alpha granule lumen / Cell surface interactions at the vascular wall / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / adenylate cyclase-activating G protein-coupled receptor signaling pathway / platelet activation / cytokine-mediated signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of cell population proliferation / G alpha (i) signalling events / collagen-containing extracellular matrix / cellular response to lipopolysaccharide / inflammatory response / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytoplasm

Domain/homology:

CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta

Component:

Platelet factor 4

• Biological species: Mus musculus (house mouse); Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.74 Å
• Authors: Cai, Z. / Zhu, Z. / Liu, Q. / Greene, M.I.
• Citation: Journal: To be Published; Title: crystal structure of RTOFab in complex with platelet factor 4; Authors: Cai, Z. / Zhu, Z. / Liu, Q. / Greene, M.I.

History

Deposition	Sep 11, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 16, 2016	Provider: repository / Type: Initial release

Assembly

Deposited unit

A: RTOFab light chain

B: RTOFab heavy chain

C: Platelet factor 4

D: RTOFab light chain

E: RTOFab heavy chain

F: Platelet factor 4

G: RTOFab light chain

H: RTOFab heavy chain

I: Platelet factor 4

J: RTOFab light chain

K: RTOFab heavy chain

L: Platelet factor 4

M: RTOFab light chain

N: RTOFab heavy chain

O: Platelet factor 4

P: RTOFab light chain

Q: RTOFab heavy chain

R: Platelet factor 4

S: RTOFab light chain

T: RTOFab heavy chain

U: Platelet factor 4

V: RTOFab light chain

W: RTOFab heavy chain

X: Platelet factor 4

Summary:

• 439 kDa, 24 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	438,555	24
Polymers	438,555	24
Non-polymers	0	0
Water	0

1

A: RTOFab light chain

B: RTOFab heavy chain

C: Platelet factor 4

Summary:

• defined by author
• 54.8 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	54,819	3
Polymers	54,819	3
Non-polymers	0	0
Water	0

Symmetry operations:

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

Calculated values:

Buried area	12980 Å2
ΔGint	-80 kcal/mol
Surface area	45170 Å2

2

D: RTOFab light chain

E: RTOFab heavy chain

F: Platelet factor 4

Summary:

• defined by author
• 54.8 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	54,819	3
Polymers	54,819	3
Non-polymers	0	0
Water	0

Symmetry operations:

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

Calculated values:

Buried area	12840 Å2
ΔGint	-79 kcal/mol
Surface area	45200 Å2

3

G: RTOFab light chain

H: RTOFab heavy chain

I: Platelet factor 4

Summary:

• defined by author
• 54.8 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	54,819	3
Polymers	54,819	3
Non-polymers	0	0
Water	0

Symmetry operations:

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

Calculated values:

Buried area	12970 Å2
ΔGint	-79 kcal/mol
Surface area	45190 Å2

4

J: RTOFab light chain

K: RTOFab heavy chain

L: Platelet factor 4

Summary:

• defined by author
• 54.8 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	54,819	3
Polymers	54,819	3
Non-polymers	0	0
Water	0

Symmetry operations:

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

Calculated values:

Buried area	12890 Å2
ΔGint	-78 kcal/mol
Surface area	45280 Å2

5

M: RTOFab light chain

N: RTOFab heavy chain

O: Platelet factor 4

Summary:

• defined by author
• 54.8 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	54,819	3
Polymers	54,819	3
Non-polymers	0	0
Water	0

Symmetry operations:

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

6

P: RTOFab light chain

Q: RTOFab heavy chain

R: Platelet factor 4

Summary:

• defined by author
• 54.8 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	54,819	3
Polymers	54,819	3
Non-polymers	0	0
Water	0

Symmetry operations:

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

7

S: RTOFab light chain

T: RTOFab heavy chain

U: Platelet factor 4

Summary:

• defined by author
• 54.8 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	54,819	3
Polymers	54,819	3
Non-polymers	0	0
Water	0

Symmetry operations:

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

8

V: RTOFab light chain

W: RTOFab heavy chain

X: Platelet factor 4

Summary:

• defined by author
• 54.8 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	54,819	3
Polymers	54,819	3
Non-polymers	0	0
Water	0

Symmetry operations:

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

Unit cell

Length a, b, c (Å)	161.424, 171.873, 208.159
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P21212

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	D
1	2	A
2	2	G
1	3	A
2	3	J
1	4	A
2	4	M
1	5	A
2	5	P
1	6	A
2	6	S
1	7	A
2	7	V
1	8	B
2	8	E
1	9	B
2	9	H
1	10	B
2	10	K
1	11	B
2	11	N
1	12	B
2	12	Q
1	13	B
2	13	T
1	14	B
2	14	W
1	15	C
2	15	F
1	16	C
2	16	I
1	17	C
2	17	L
1	18	C
2	18	O
1	19	C
2	19	R
1	20	C
2	20	U
1	21	C
2	21	X
1	22	D
2	22	G
1	23	D
2	23	J
1	24	D
2	24	M
1	25	D
2	25	P
1	26	D
2	26	S
1	27	D
2	27	V
1	28	E
2	28	H
1	29	E
2	29	K
1	30	E
2	30	N
1	31	E
2	31	Q
1	32	E
2	32	T
1	33	E
2	33	W
1	34	F
2	34	I
1	35	F
2	35	L
1	36	F
2	36	O
1	37	F
2	37	R
1	38	F
2	38	U
1	39	F
2	39	X
1	40	G
2	40	J
1	41	G
2	41	M
1	42	G
2	42	P
1	43	G
2	43	S
1	44	G
2	44	V
1	45	H
2	45	K
1	46	H
2	46	N
1	47	H
2	47	Q
1	48	H
2	48	T
1	49	H
2	49	W
1	50	I
2	50	L
1	51	I
2	51	O
1	52	I
2	52	R
1	53	I
2	53	U
1	54	I
2	54	X
1	55	J
2	55	M
1	56	J
2	56	P
1	57	J
2	57	S
1	58	J
2	58	V
1	59	K
2	59	N
1	60	K
2	60	Q
1	61	K
2	61	T
1	62	K
2	62	W
1	63	L
2	63	O
1	64	L
2	64	R
1	65	L
2	65	U
1	66	L
2	66	X
1	67	M
2	67	P
1	68	M
2	68	S
1	69	M
2	69	V
1	70	N
2	70	Q
1	71	N
2	71	T
1	72	N
2	72	W
1	73	O
2	73	R
1	74	O
2	74	U
1	75	O
2	75	X
1	76	P
2	76	S
1	77	P
2	77	V
1	78	Q
2	78	T
1	79	Q
2	79	W
1	80	R
2	80	U
1	81	R
2	81	X
1	82	S
2	82	V
1	83	T
2	83	W
1	84	U
2	84	X

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	3 - 214
2	0	1	0	D	3 - 214
1	0	2	0	A	3 - 214
2	0	2	0	G	3 - 214
1	0	3	0	A	3 - 214
2	0	3	0	J	3 - 214
1	0	4	0	A	3 - 214
2	0	4	0	M	3 - 214
1	0	5	0	A	3 - 214
2	0	5	0	P	3 - 214
1	0	6	0	A	3 - 214
2	0	6	0	S	3 - 214
1	0	7	0	A	3 - 214
2	0	7	0	V	3 - 214
1	0	8	0	B	3 - 221
2	0	8	0	E	3 - 221
1	0	9	0	B	3 - 221
2	0	9	0	H	3 - 221
1	0	10	0	B	3 - 221
2	0	10	0	K	3 - 221
1	0	11	0	B	3 - 221
2	0	11	0	N	3 - 221
1	0	12	0	B	3 - 221
2	0	12	0	Q	3 - 221
1	0	13	0	B	3 - 221
2	0	13	0	T	3 - 221
1	0	14	0	B	3 - 221
2	0	14	0	W	3 - 221
1	0	15	0	C	4 - 68
2	0	15	0	F	4 - 68
1	0	16	0	C	4 - 67
2	0	16	0	I	4 - 67
1	0	17	0	C	4 - 68
2	0	17	0	L	4 - 68
1	0	18	0	C	4 - 68
2	0	18	0	O	4 - 68
1	0	19	0	C	4 - 68
2	0	19	0	R	4 - 68
1	0	20	0	C	4 - 68
2	0	20	0	U	4 - 68
1	0	21	0	C	4 - 67
2	0	21	0	X	4 - 67
1	0	22	0	D	3 - 214
2	0	22	0	G	3 - 214
1	0	23	0	D	3 - 214
2	0	23	0	J	3 - 214
1	0	24	0	D	3 - 214
2	0	24	0	M	3 - 214
1	0	25	0	D	3 - 214
2	0	25	0	P	3 - 214
1	0	26	0	D	3 - 214
2	0	26	0	S	3 - 214
1	0	27	0	D	3 - 214
2	0	27	0	V	3 - 214
1	0	28	0	E	3 - 221
2	0	28	0	H	3 - 221
1	0	29	0	E	3 - 221
2	0	29	0	K	3 - 221
1	0	30	0	E	3 - 221
2	0	30	0	N	3 - 221
1	0	31	0	E	3 - 221
2	0	31	0	Q	3 - 221
1	0	32	0	E	3 - 221
2	0	32	0	T	3 - 221
1	0	33	0	E	3 - 221
2	0	33	0	W	3 - 221
1	0	34	0	F	4 - 67
2	0	34	0	I	4 - 67
1	0	35	0	F	4 - 68
2	0	35	0	L	4 - 68
1	0	36	0	F	4 - 68
2	0	36	0	O	4 - 68
1	0	37	0	F	4 - 68
2	0	37	0	R	4 - 68
1	0	38	0	F	4 - 68
2	0	38	0	U	4 - 68
1	0	39	0	F	4 - 67
2	0	39	0	X	4 - 67
1	0	40	0	G	3 - 214
2	0	40	0	J	3 - 214
1	0	41	0	G	3 - 214
2	0	41	0	M	3 - 214
1	0	42	0	G	3 - 214
2	0	42	0	P	3 - 214
1	0	43	0	G	3 - 214
2	0	43	0	S	3 - 214
1	0	44	0	G	3 - 214
2	0	44	0	V	3 - 214
1	0	45	0	H	3 - 221
2	0	45	0	K	3 - 221
1	0	46	0	H	3 - 221
2	0	46	0	N	3 - 221
1	0	47	0	H	3 - 221
2	0	47	0	Q	3 - 221
1	0	48	0	H	3 - 221
2	0	48	0	T	3 - 221
1	0	49	0	H	3 - 221
2	0	49	0	W	3 - 221
1	0	50	0	I	4 - 67
2	0	50	0	L	4 - 67
1	0	51	0	I	4 - 67
2	0	51	0	O	4 - 67
1	0	52	0	I	4 - 67
2	0	52	0	R	4 - 67
1	0	53	0	I	4 - 67
2	0	53	0	U	4 - 67
1	0	54	0	I	4 - 69
2	0	54	0	X	4 - 69
1	0	55	0	J	3 - 214
2	0	55	0	M	3 - 214
1	0	56	0	J	3 - 214
2	0	56	0	P	3 - 214
1	0	57	0	J	3 - 214
2	0	57	0	S	3 - 214
1	0	58	0	J	3 - 214
2	0	58	0	V	3 - 214
1	0	59	0	K	3 - 221
2	0	59	0	N	3 - 221
1	0	60	0	K	3 - 221
2	0	60	0	Q	3 - 221
1	0	61	0	K	3 - 221
2	0	61	0	T	3 - 221
1	0	62	0	K	3 - 221
2	0	62	0	W	3 - 221
1	0	63	0	L	4 - 68
2	0	63	0	O	4 - 68
1	0	64	0	L	4 - 68
2	0	64	0	R	4 - 68
1	0	65	0	L	4 - 68
2	0	65	0	U	4 - 68
1	0	66	0	L	4 - 67
2	0	66	0	X	4 - 67
1	0	67	0	M	3 - 214
2	0	67	0	P	3 - 214
1	0	68	0	M	3 - 214
2	0	68	0	S	3 - 214
1	0	69	0	M	3 - 214
2	0	69	0	V	3 - 214
1	0	70	0	N	3 - 221
2	0	70	0	Q	3 - 221
1	0	71	0	N	3 - 221
2	0	71	0	T	3 - 221
1	0	72	0	N	3 - 221
2	0	72	0	W	3 - 221
1	0	73	0	O	4 - 68
2	0	73	0	R	4 - 68
1	0	74	0	O	4 - 68
2	0	74	0	U	4 - 68
1	0	75	0	O	4 - 67
2	0	75	0	X	4 - 67
1	0	76	0	P	3 - 214
2	0	76	0	S	3 - 214
1	0	77	0	P	3 - 214
2	0	77	0	V	3 - 214
1	0	78	0	Q	3 - 221
2	0	78	0	T	3 - 221
1	0	79	0	Q	3 - 221
2	0	79	0	W	3 - 221
1	0	80	0	R	4 - 68
2	0	80	0	U	4 - 68
1	0	81	0	R	4 - 67
2	0	81	0	X	4 - 67
1	0	82	0	S	3 - 214
2	0	82	0	V	3 - 214
1	0	83	0	T	3 - 221
2	0	83	0	W	3 - 221
1	0	84	0	U	4 - 67
2	0	84	0	X	4 - 67

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

Components

#1: Antibody

A D G J M P S V
RTOFab light chain

Details:

Mass: 23383.781 Da / Num. of mol.: 8 / Fragment: UNP residues 32-101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

#2: Antibody

B E H K N Q T W
RTOFab heavy chain

Details:

Mass: 23653.461 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

#3: Protein

C F I L O R U X
Platelet factor 4 / / PF-4 / C-X-C motif chemokine 4 / Iroplact / Oncostatin-A / Platelet factor 4 / short form

Details:

Mass: 7782.195 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PF4, CXCL4, SCYB4 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P02776

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 3.24 ų/Da / Density % sol: 61.99 %
• Crystal grow: Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 ; Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS, pH 6.5, 25% w/v Polyethylene glycol 3350., VAPOR DIFFUSION, HANGING DROP, temperature 289K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 2.07 Å
• Detector: Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 23, 2014
• Radiation: Monochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 2.07 Å / Relative weight: 1
• Reflection: Resolution: 3.74→50 Å / Num. all: 60619 / Num. obs: 60223 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

Reflection shell

Resolution (Å)	Redundancy (%)	Rmerge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
3.75-3.81	25.6	0	2.9	1	98.9
3.81-3.88	25.6	0	4.2	1	98.6
3.88-3.96	25.5	0.965	5.6	1	98.6
3.96-4.04	25.9	0	4.6	1	99.1
4.04-4.13	26.2	0.765	7.1	1	99.3
4.13-4.22	26.5	0.589	9	1	99.1

Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.8.0049	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.74→50 Å / Cor.coef. F_o:F_c: 0.902 / Cor.coef. F_o:F_c free: 0.887 / SU B: 38.049 / SU ML: 0.511 / Cross valid method: THROUGHOUT / ESU R Free: 0.792 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.28444	3011	5 %	RANDOM
Rwork	0.24326	-	-	-
obs	0.24533	56670	98.51 %	-

• 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: 136.355 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-2.43 Å2	0 Å2	0 Å2
2-	-	8.55 Å2	0 Å2
3-	-	-	-6.11 Å2

Refinement step

Cycle: LAST / Resolution: 3.74→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30074	0	0	0	30074

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.02	30794
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	28145
X-RAY DIFFRACTION	r_angle_refined_deg	1.278	1.96	41909
X-RAY DIFFRACTION	r_angle_other_deg	1.081	3	65115
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.304	5	3946
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.67	23.738	1137
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.259	15	4920
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.297	15	144
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	4784
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	34666
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	6786
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	6.095	13.814	15856
X-RAY DIFFRACTION	r_mcbond_other	6.093	13.814	15855
X-RAY DIFFRACTION	r_mcangle_it	10.054	20.715	19778
X-RAY DIFFRACTION	r_mcangle_other	10.492	20.227	19779
X-RAY DIFFRACTION	r_scbond_it	5.378	14.028	14938
X-RAY DIFFRACTION	r_scbond_other	5.988	13.843	14939
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	10.233	20.562	22139
X-RAY DIFFRACTION	r_long_range_B_refined	15.678		33077
X-RAY DIFFRACTION	r_long_range_B_other	15.677		33076
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	11640	0.05
1	2	D	11640	0.05
2	1	A	11566	0.06
2	2	G	11566	0.06
3	1	A	11476	0.07
3	2	J	11476	0.07
4	1	A	11523	0.07
4	2	M	11523	0.07
5	1	A	11590	0.07
5	2	P	11590	0.07
6	1	A	11479	0.07
6	2	S	11479	0.07
7	1	A	11489	0.07
7	2	V	11489	0.07
8	1	B	11276	0.04
8	2	E	11276	0.04
9	1	B	11342	0.03
9	2	H	11342	0.03
10	1	B	11251	0.04
10	2	K	11251	0.04
11	1	B	11262	0.04
11	2	N	11262	0.04
12	1	B	11269	0.04
12	2	Q	11269	0.04
13	1	B	11303	0.04
13	2	T	11303	0.04
14	1	B	11325	0.03
14	2	W	11325	0.03
15	1	C	3959	0.03
15	2	F	3959	0.03
16	1	C	3733	0.05
16	2	I	3733	0.05
17	1	C	3752	0.08
17	2	L	3752	0.08
18	1	C	3941	0.05
18	2	O	3941	0.05
19	1	C	3955	0.03
19	2	R	3955	0.03
20	1	C	3840	0.06
20	2	U	3840	0.06
21	1	C	3783	0.06
21	2	X	3783	0.06
22	1	D	11420	0.08
22	2	G	11420	0.08
23	1	D	11434	0.07
23	2	J	11434	0.07
24	1	D	11409	0.07
24	2	M	11409	0.07
25	1	D	11421	0.07
25	2	P	11421	0.07
26	1	D	11324	0.08
26	2	S	11324	0.08
27	1	D	11529	0.07
27	2	V	11529	0.07
28	1	E	11316	0.05
28	2	H	11316	0.05
29	1	E	11269	0.03
29	2	K	11269	0.03
30	1	E	11253	0.05
30	2	N	11253	0.05
31	1	E	11254	0.05
31	2	Q	11254	0.05
32	1	E	11291	0.04
32	2	T	11291	0.04
33	1	E	11317	0.04
33	2	W	11317	0.04
34	1	F	3740	0.05
34	2	I	3740	0.05
35	1	F	3748	0.08
35	2	L	3748	0.08
36	1	F	3939	0.06
36	2	O	3939	0.06
37	1	F	3960	0.03
37	2	R	3960	0.03
38	1	F	3831	0.07
38	2	U	3831	0.07
39	1	F	3781	0.06
39	2	X	3781	0.06
40	1	G	11486	0.07
40	2	J	11486	0.07
41	1	G	11425	0.07
41	2	M	11425	0.07
42	1	G	11429	0.07
42	2	P	11429	0.07
43	1	G	11465	0.07
43	2	S	11465	0.07
44	1	G	11544	0.07
44	2	V	11544	0.07
45	1	H	11297	0.04
45	2	K	11297	0.04
46	1	H	11295	0.04
46	2	N	11295	0.04
47	1	H	11288	0.04
47	2	Q	11288	0.04
48	1	H	11336	0.04
48	2	T	11336	0.04
49	1	H	11360	0.03
49	2	W	11360	0.03
50	1	I	3585	0.08
50	2	L	3585	0.08
51	1	I	3712	0.07
51	2	O	3712	0.07
52	1	I	3736	0.05
52	2	R	3736	0.05
53	1	I	3677	0.07
53	2	U	3677	0.07
54	1	I	3786	0.08
54	2	X	3786	0.08
55	1	J	11352	0.08
55	2	M	11352	0.08
56	1	J	11412	0.07
56	2	P	11412	0.07
57	1	J	11429	0.07
57	2	S	11429	0.07
58	1	J	11446	0.07
58	2	V	11446	0.07
59	1	K	11229	0.05
59	2	N	11229	0.05
60	1	K	11230	0.05
60	2	Q	11230	0.05
61	1	K	11290	0.04
61	2	T	11290	0.04
62	1	K	11317	0.03
62	2	W	11317	0.03
63	1	L	3738	0.09
63	2	O	3738	0.09
64	1	L	3746	0.08
64	2	R	3746	0.08
65	1	L	3698	0.09
65	2	U	3698	0.09
66	1	L	3645	0.08
66	2	X	3645	0.08
67	1	M	11449	0.07
67	2	P	11449	0.07
68	1	M	11441	0.07
68	2	S	11441	0.07
69	1	M	11471	0.07
69	2	V	11471	0.07
70	1	N	11266	0.05
70	2	Q	11266	0.05
71	1	N	11262	0.04
71	2	T	11262	0.04
72	1	N	11292	0.04
72	2	W	11292	0.04
73	1	O	3934	0.06
73	2	R	3934	0.06
74	1	O	3814	0.08
74	2	U	3814	0.08
75	1	O	3772	0.07
75	2	X	3772	0.07
76	1	P	11421	0.07
76	2	S	11421	0.07
77	1	P	11401	0.08
77	2	V	11401	0.08
78	1	Q	11273	0.05
78	2	T	11273	0.05
79	1	Q	11301	0.04
79	2	W	11301	0.04
80	1	R	3829	0.07
80	2	U	3829	0.07
81	1	R	3780	0.06
81	2	X	3780	0.06
82	1	S	11485	0.07
82	2	V	11485	0.07
83	1	T	11390	0.02
83	2	W	11390	0.02
84	1	U	3704	0.08
84	2	X	3704	0.08

LS refinement shell

Resolution: 3.739→3.836 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.38	223	-
Rwork	0.356	4097	-
obs	-	-	97.98 %