PDB-3my0: Crystal structure of the ACVRL1 (ALK1) kinase domain bound to LDN...

Basic information

• Entry: Database: PDB / ID: 3my0
• Title: Crystal structure of the ACVRL1 (ALK1) kinase domain bound to LDN-193189
• Components: Serine/threonine-protein kinase receptor R3
• Keywords: TRANSFERASE / Protein Kinase / Serine/threonine-protein kinase receptor / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function:

lymphatic endothelial cell differentiation / regulation of endothelial cell proliferation / negative regulation of endothelial cell differentiation / dorsal aorta morphogenesis / positive regulation of epithelial cell differentiation / blood vessel maturation / lymphangiogenesis / venous blood vessel development / transforming growth factor beta receptor activity / retina vasculature development in camera-type eye / positive regulation of chondrocyte differentiation / BMP receptor complex / BMP receptor activity / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of endothelial cell differentiation / activin receptor activity, type I / transforming growth factor beta receptor activity, type I / endothelial tube morphogenesis / negative regulation of focal adhesion assembly / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / artery development / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / activin binding / cellular response to BMP stimulus / positive regulation of BMP signaling pathway / negative regulation of cell adhesion / transforming growth factor beta binding / dorsal/ventral pattern formation / negative regulation of endothelial cell migration / blood circulation / wound healing, spreading of epidermal cells / endocardial cushion morphogenesis / negative regulation of endothelial cell proliferation / positive regulation of Notch signaling pathway / SMAD binding / negative regulation of blood vessel endothelial cell migration / regulation of DNA replication / positive regulation of SMAD protein signal transduction / blood vessel remodeling / BMP signaling pathway / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / negative regulation of cell growth / cellular response to growth factor stimulus / regulation of blood pressure / positive regulation of angiogenesis / heart development / angiogenesis / in utero embryonic development / response to hypoxia / negative regulation of cell population proliferation / phosphorylation / negative regulation of gene expression / protein serine/threonine kinase activity / dendrite / neuronal cell body / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / plasma membrane

Domain/homology:

GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta

Component:

Chem-LDN / Serine/threonine-protein kinase receptor R3

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
• Authors: Chaikuad, A. / Alfano, I. / Cooper, C. / Mahajan, P. / Daga, N. / Sanvitale, C. / Fedorov, O. / Petrie, K. / Savitsky, P. / Gileadi, O. / Sethi, R. / Krojer, T. / Muniz, J.R.C. / Pike, A.C.W. / Vollmar, M. / Carpenter, C.P. / Ugochukwu, E. / Knapp, S. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
• Citation: Journal: Angiogenesis / Year: 2015; Title: A small molecule targeting ALK1 prevents Notch cooperativity and inhibits functional angiogenesis.; Authors: Kerr, G. / Sheldon, H. / Chaikuad, A. / Alfano, I. / von Delft, F. / Bullock, A.N. / Harris, A.L.

History

Deposition	May 8, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 21, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Apr 1, 2015	Group: Database references
Revision 1.3	Nov 1, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Serine/threonine-protein kinase receptor R3

B: Serine/threonine-protein kinase receptor R3

C: Serine/threonine-protein kinase receptor R3

D: Serine/threonine-protein kinase receptor R3

E: Serine/threonine-protein kinase receptor R3

F: Serine/threonine-protein kinase receptor R3

G: Serine/threonine-protein kinase receptor R3

H: Serine/threonine-protein kinase receptor R3

I: Serine/threonine-protein kinase receptor R3

J: Serine/threonine-protein kinase receptor R3

K: Serine/threonine-protein kinase receptor R3

L: Serine/threonine-protein kinase receptor R3

M: Serine/threonine-protein kinase receptor R3

N: Serine/threonine-protein kinase receptor R3

O: Serine/threonine-protein kinase receptor R3

P: Serine/threonine-protein kinase receptor R3

Q: Serine/threonine-protein kinase receptor R3

R: Serine/threonine-protein kinase receptor R3

S: Serine/threonine-protein kinase receptor R3

T: Serine/threonine-protein kinase receptor R3

U: Serine/threonine-protein kinase receptor R3

V: Serine/threonine-protein kinase receptor R3

W: Serine/threonine-protein kinase receptor R3

X: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• 845 kDa, 24 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	845,165	48
Polymers	835,409	24
Non-polymers	9,756	24
Water	2,270	126

1

A: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

2

B: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

3

C: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

4

D: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

5

E: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

6

F: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

7

G: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

8

H: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

9

I: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

10

J: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

11

K: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	0

Symmetry operations:

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

Calculated values:

Method	PISA

12

L: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

13

M: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

14

N: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

15

O: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

16

P: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

17

Q: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

18

R: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

19

S: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

20

T: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

21

U: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

22

V: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

23

W: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

24

X: Serine/threonine-protein kinase receptor R3

hetero molecules

Summary:

• defined by author&software
• 35.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,215	2
Polymers	34,809	1
Non-polymers	406	1
Water	0

Symmetry operations:

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

Calculated values:

Method	PISA

Unit cell

Length a, b, c (Å)	118.770, 118.770, 510.791
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P32

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	G
3	1	B
4	1	C
5	1	D
6	1	E
7	1	F
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L
13	1	M
14	1	N
15	1	O
1	2	C
2	2	A
3	2	B
4	2	D
5	2	E
6	2	F
7	2	G
8	2	H
9	2	I
10	2	J
11	2	K
12	2	L
13	2	M
14	2	N
15	2	O
1	3	E
2	3	A
3	3	B
4	3	C
5	3	D
6	3	I
7	3	F
8	3	G
9	3	H
10	3	J
11	3	K
12	3	L
13	3	M
14	3	N
15	3	O
1	4	A
2	4	I
3	4	B
4	4	E
5	4	F
6	4	G
7	4	K
8	4	T
9	4	L
10	4	M
11	4	Q
12	4	R
13	4	U
14	4	W
15	4	X
1	5	C
2	5	D
3	5	H
4	5	N
5	5	O
6	5	S
1	6	C
2	6	D
3	6	N
4	6	O

NCS ensembles :

ID
1
2
3
4
5
6

Components

#1: Protein

A B C D E F G H I J K L M N O P Q R S ...
Serine/threonine-protein kinase receptor R3 / SKR3 / Activin receptor-like kinase 1 / ALK-1 / TGF-B superfamily receptor type I / TSR-I

Details:

Mass: 34808.719 Da / Num. of mol.: 24 / Fragment: kinase domain (UNP residue 195-497)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVRL1, ACVRL1 (ALK1), ACVRLK1, ALK1 / Plasmid: pFB-LIC-Bse / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P37023, receptor protein serine/threonine kinase

#2: Chemical

A-600 B-600 C-600 D-600 E-600 F-600 G-600 H-600 I-600 J-600 K-600 L-600 M-600 N-600 O-600 P-600 Q-600 R-600 S-600 T-600 ...
ChemComp-LDN / 4-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline / LDN193189

Details:

Mass: 406.482 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₂₅H₂₂N₆

#3: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.49 ų/Da / Density % sol: 50.6 %
• Crystal grow: Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 ; Details: 16% PEG 3350, 0.2M Na/K PO4, 5% ethylene glycol, 2% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9779 Å
• Detector: Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2010 / Details: two K-B pairs of bimorph type mirrors
• Radiation: Monochromator: ACCEL Fixed exit Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9779 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.357
1	1	h+k,-k,-l	2	0.147
1	1	-h,-k,l	3	0.352
1	1	h,-h-k,-l	4	0.145

• Reflection: Resolution: 2.65→58.99 Å / Num. all: 233884 / Num. obs: 233740 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / B_iso Wilson estimate: 56 Ų / R_merge(I) obs: 0.153 / Net I/σ(I): 7.8
• Reflection shell: Resolution: 2.65→2.79 Å / Redundancy: 3 % / R_merge(I) obs: 0.593 / Mean I/σ(I) obs: 2 / Num. unique all: 34027 / % possible all: 99.5

Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.6.0066	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H9R

3h9r

Resolution: 2.65→58.99 Å / Cor.coef. F_o:F_c: 0.912 / Cor.coef. F_o:F_c free: 0.883 / SU B: 14.462 / SU ML: 0.151 / SU R_free: 0.358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.24707	12110	5.2 %	RANDOM
Rwork	0.20701	-	-	-
obs	0.2091	221623	99.71 %	-
all	-	233740	-	-

• 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: 37.583 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	7.81 Å2	0 Å2	0 Å2
2-	-	7.81 Å2	0 Å2
3-	-	-	-15.61 Å2

Refinement step

Cycle: LAST / Resolution: 2.65→58.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	53061	0	744	126	53931

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	55226
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	35975
X-RAY DIFFRACTION	r_angle_refined_deg	1.27	1.955	75354
X-RAY DIFFRACTION	r_angle_other_deg	0.978	3.002	86711
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.24	5	6867
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.2	23.236	2284
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.571	15	8241
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.965	15	338
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	8411
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	61833
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	11357

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	2048	tight positional	0.05	0.05
1	1	B	2048	tight positional	0.04	0.05
1	1	C	2048	tight positional	0.03	0.05
1	1	D	2048	tight positional	0.04	0.05
1	1	E	2048	tight positional	0.04	0.05
1	1	F	2048	tight positional	0.04	0.05
1	1	G	2048	tight positional	0.03	0.05
1	1	H	2048	tight positional	0.08	0.05
1	1	I	2048	tight positional	0.04	0.05
1	1	J	2048	tight positional	0.02	0.05
1	1	K	2048	tight positional	0.02	0.05
1	1	L	2048	tight positional	0.04	0.05
1	1	M	2048	tight positional	0.04	0.05
1	1	N	2048	tight positional	0.05	0.05
1	1	O	2048	tight positional	0.04	0.05
1	1	P	2048	tight positional	0.02	0.05
1	1	Q	2048	tight positional	0.04	0.05
1	1	R	2048	tight positional	0.04	0.05
1	1	S	2048	tight positional	0.04	0.05
1	1	T	2048	tight positional	0.03	0.05
1	1	U	2048	tight positional	0.04	0.05
1	1	V	2048	tight positional	0.03	0.05
1	1	W	2048	tight positional	0.03	0.05
1	1	X	2048	tight positional	0.02	0.05
2	2	A	362	tight positional	0.04	0.05
2	2	B	362	tight positional	0.03	0.05
2	2	C	362	tight positional	0.03	0.05
2	2	D	362	tight positional	0.04	0.05
2	2	E	362	tight positional	0.03	0.05
2	2	F	362	tight positional	0.03	0.05
2	2	G	362	tight positional	0.03	0.05
2	2	H	362	tight positional	0.03	0.05
2	2	I	362	tight positional	0.04	0.05
2	2	J	362	tight positional	0.02	0.05
2	2	K	362	tight positional	0.02	0.05
2	2	L	362	tight positional	0.03	0.05
2	2	M	362	tight positional	0.04	0.05
2	2	N	362	tight positional	0.04	0.05
2	2	O	362	tight positional	0.03	0.05
2	2	P	362	tight positional	0.02	0.05
2	2	Q	362	tight positional	0.03	0.05
2	2	R	362	tight positional	0.03	0.05
2	2	S	362	tight positional	0.04	0.05
2	2	T	362	tight positional	0.03	0.05
2	2	U	362	tight positional	0.03	0.05
2	2	V	362	tight positional	0.04	0.05
2	2	W	362	tight positional	0.04	0.05
2	2	X	362	tight positional	0.02	0.05
3	3	A	71	tight positional	0.04	0.05
3	3	B	71	tight positional	0.04	0.05
3	3	C	71	tight positional	0.03	0.05
3	3	D	71	tight positional	0.04	0.05
3	3	E	71	tight positional	0.05	0.05
3	3	F	71	tight positional	0.03	0.05
3	3	G	71	tight positional	0.03	0.05
3	3	H	71	tight positional	0.03	0.05
3	3	I	71	tight positional	0.05	0.05
3	3	J	71	tight positional	0.03	0.05
3	3	K	71	tight positional	0.02	0.05
3	3	L	71	tight positional	0.03	0.05
3	3	M	71	tight positional	0.03	0.05
3	3	N	71	tight positional	0.04	0.05
3	3	O	71	tight positional	0.03	0.05
3	3	P	71	tight positional	0.04	0.05
3	3	Q	71	tight positional	0.03	0.05
3	3	R	71	tight positional	0.04	0.05
3	3	S	71	tight positional	0.04	0.05
3	3	T	71	tight positional	0.04	0.05
3	3	U	71	tight positional	0.03	0.05
3	3	V	71	tight positional	0.05	0.05
3	3	W	71	tight positional	0.03	0.05
3	3	X	71	tight positional	0.04	0.05
4	4	A	71	tight positional	0.04	0.05
4	4	I	71	tight positional	0.04	0.05
4	4	B	71	tight positional	0.03	0.05
4	4	E	71	tight positional	0.04	0.05
4	4	F	71	tight positional	0.04	0.05
4	4	G	71	tight positional	0.04	0.05
4	4	K	71	tight positional	0.02	0.05
4	4	T	71	tight positional	0.03	0.05
4	4	L	71	tight positional	0.03	0.05
4	4	M	71	tight positional	0.03	0.05
4	4	Q	71	tight positional	0.04	0.05
4	4	R	71	tight positional	0.04	0.05
4	4	U	71	tight positional	0.03	0.05
4	4	W	71	tight positional	0.03	0.05
4	4	X	71	tight positional	0.02	0.05
5	5	C	202	tight positional	0.03	0.05
5	5	D	202	tight positional	0.03	0.05
5	5	H	202	tight positional	0.03	0.05
5	5	N	202	tight positional	0.03	0.05
5	5	O	202	tight positional	0.03	0.05
5	5	S	202	tight positional	0.03	0.05
6	6	C	98	tight positional	0.04	0.05
6	6	D	98	tight positional	0.06	0.05
6	6	N	98	tight positional	0.05	0.05
6	6	O	98	tight positional	0.04	0.05
1	1	A	2048	tight thermal	5.06	0.5
1	1	B	2048	tight thermal	7.14	0.5
1	1	C	2048	tight thermal	3.88	0.5
1	1	D	2048	tight thermal	4.39	0.5
1	1	E	2048	tight thermal	4.34	0.5
1	1	F	2048	tight thermal	4.79	0.5
1	1	G	2048	tight thermal	5.72	0.5
1	1	H	2048	tight thermal	4.68	0.5
1	1	I	2048	tight thermal	7.27	0.5
1	1	J	2048	tight thermal	18.16	0.5
1	1	K	2048	tight thermal	20.77	0.5
1	1	L	2048	tight thermal	5.11	0.5
1	1	M	2048	tight thermal	5.31	0.5
1	1	N	2048	tight thermal	7.68	0.5
1	1	O	2048	tight thermal	4.2	0.5
1	1	P	2048	tight thermal	17.79	0.5
1	1	Q	2048	tight thermal	4.86	0.5
1	1	R	2048	tight thermal	4.36	0.5
1	1	S	2048	tight thermal	6.81	0.5
1	1	T	2048	tight thermal	3.96	0.5
1	1	U	2048	tight thermal	4.73	0.5
1	1	V	2048	tight thermal	4.61	0.5
1	1	W	2048	tight thermal	4.51	0.5
1	1	X	2048	tight thermal	20.95	0.5
2	2	A	362	tight thermal	3.28	0.5
2	2	B	362	tight thermal	3.2	0.5
2	2	C	362	tight thermal	4.59	0.5
2	2	D	362	tight thermal	8.73	0.5
2	2	E	362	tight thermal	5.38	0.5
2	2	F	362	tight thermal	5.81	0.5
2	2	G	362	tight thermal	5.09	0.5
2	2	H	362	tight thermal	3.6	0.5
2	2	I	362	tight thermal	8.43	0.5
2	2	J	362	tight thermal	13.01	0.5
2	2	K	362	tight thermal	17.45	0.5
2	2	L	362	tight thermal	4.63	0.5
2	2	M	362	tight thermal	5.4	0.5
2	2	N	362	tight thermal	7.38	0.5
2	2	O	362	tight thermal	3.76	0.5
2	2	P	362	tight thermal	16.39	0.5
2	2	Q	362	tight thermal	3.9	0.5
2	2	R	362	tight thermal	3.66	0.5
2	2	S	362	tight thermal	7.19	0.5
2	2	T	362	tight thermal	3.14	0.5
2	2	U	362	tight thermal	6.26	0.5
2	2	V	362	tight thermal	5.61	0.5
2	2	W	362	tight thermal	4.49	0.5
2	2	X	362	tight thermal	21.17	0.5
3	3	A	71	tight thermal	5.55	0.5
3	3	B	71	tight thermal	3.61	0.5
3	3	C	71	tight thermal	4.65	0.5
3	3	D	71	tight thermal	9.2	0.5
3	3	E	71	tight thermal	5.35	0.5
3	3	F	71	tight thermal	4.77	0.5
3	3	G	71	tight thermal	3.55	0.5
3	3	H	71	tight thermal	2.99	0.5
3	3	I	71	tight thermal	8.3	0.5
3	3	J	71	tight thermal	16.06	0.5
3	3	K	71	tight thermal	17.34	0.5
3	3	L	71	tight thermal	3.92	0.5
3	3	M	71	tight thermal	8.08	0.5
3	3	N	71	tight thermal	8.9	0.5
3	3	O	71	tight thermal	3.87	0.5
3	3	P	71	tight thermal	20.01	0.5
3	3	Q	71	tight thermal	4.46	0.5
3	3	R	71	tight thermal	4.37	0.5
3	3	S	71	tight thermal	8.52	0.5
3	3	T	71	tight thermal	2.05	0.5
3	3	U	71	tight thermal	2.89	0.5
3	3	V	71	tight thermal	4.81	0.5
3	3	W	71	tight thermal	4.72	0.5
3	3	X	71	tight thermal	22.44	0.5
4	4	A	71	tight thermal	4.7	0.5
4	4	I	71	tight thermal	5.03	0.5
4	4	B	71	tight thermal	4.4	0.5
4	4	E	71	tight thermal	2.16	0.5
4	4	F	71	tight thermal	4.5	0.5
4	4	G	71	tight thermal	8.83	0.5
4	4	K	71	tight thermal	18.52	0.5
4	4	T	71	tight thermal	2.8	0.5
4	4	L	71	tight thermal	4.07	0.5
4	4	M	71	tight thermal	1.92	0.5
4	4	Q	71	tight thermal	3.39	0.5
4	4	R	71	tight thermal	4.16	0.5
4	4	U	71	tight thermal	9.39	0.5
4	4	W	71	tight thermal	4.11	0.5
4	4	X	71	tight thermal	8.47	0.5
5	5	C	202	tight thermal	4.21	0.5
5	5	D	202	tight thermal	2.3	0.5
5	5	H	202	tight thermal	4.18	0.5
5	5	N	202	tight thermal	4.33	0.5
5	5	O	202	tight thermal	2.18	0.5
5	5	S	202	tight thermal	4.5	0.5
6	6	C	98	tight thermal	1.5	0.5
6	6	D	98	tight thermal	6.7	0.5
6	6	N	98	tight thermal	8.69	0.5
6	6	O	98	tight thermal	3.49	0.5

LS refinement shell

Resolution: 2.649→2.717 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.336	844	-
Rwork	0.258	15879	-
obs	-	-	96.84 %

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	0.5634	0.0717	0.074	0.9785	-0.0292	0.8925	-0.089	0.0758	0.0732	-0.0292	0.0255	0.1237	-0.0248	-0.0783	0.0635	0.2648	0.0072	0.0155	0.2714	-0.0119	0.142	48.5422	-55.8181	-29.5438
2	0.2499	-0.097	-0.252	1.1665	-0.2394	0.6903	-0.0479	0.091	-0.029	-0.0569	0.0254	-0.0366	-0.1606	-0.0314	0.0225	0.3527	-0.0198	0.0311	0.3099	-0.0399	0.152	62.1519	-17.0451	-16.3625
3	1.3595	-0.2633	0.1511	1.336	0.1523	1.1633	-0.0408	0.122	0.0077	-0.0356	-0.0576	0.1684	0.0316	-0.0658	0.0984	0.2712	-0.0042	0.0077	0.226	0.0006	0.0883	46.6819	15.4036	-15.0156
4	0.6989	-0.1033	-0.2402	0.8166	-0.0855	0.9119	0.0312	-0.0584	-0.0984	0.0894	-0.0293	0.0663	-0.0075	-0.0177	-0.0019	0.225	0.0307	-0.0094	0.2738	0.0232	0.1149	38.0087	-35.9063	-71.0859
5	0.2639	-0.2524	-0.5182	1.0903	0.3024	1.0662	0.0188	-0.035	0.0086	0.0548	-0.0046	-0.0698	-0.0799	0.0778	-0.0142	0.2506	-0.0157	-0.0279	0.2613	0.0001	0.1043	3.0582	-54.2824	-30.4402
6	0.5213	0.1305	0.2775	0.675	0.0187	1.7093	0.0615	0.0296	0.1966	-0.032	-0.0507	-0.061	-0.2406	0.1978	-0.0108	0.244	0.0005	0.0326	0.3651	-0.013	0.2023	74.5027	-38.6905	-56.1537
7	0.7779	-0.3115	-0.6221	1.3198	0.2953	1.6385	-0.0427	0.0303	-0.1152	-0.0528	-0.0456	-0.0032	0.0242	-0.0242	0.0882	0.1659	-0.0031	0.0147	0.1246	-0.0147	0.0204	3.3273	14.2867	-30.106
8	1.1611	-0.0324	-0.3422	0.9893	-0.2905	1.3244	0.0422	-0.0335	-0.0426	0.0286	-0.009	0.1109	0.0186	-0.0899	-0.0333	0.2526	0.0088	-0.041	0.2932	0.0184	0.0921	34.7518	34.8252	-56.3891
9	0.9898	-0.5743	-0.0959	1.1666	0.3276	1.6521	-0.0179	0.0214	0.0383	0.0314	-0.0713	0.0516	0.0036	0.0036	0.0892	0.1436	0.0026	0.0216	0.138	-0.0152	0.0152	16.7088	-7.1885	-69.4625
10	0.8718	0.0643	-0.3146	0.0088	-0.0232	0.1136	-0.0063	0.0757	-0.0516	-0.0008	-0.0137	-0.0481	0.0014	-0.0315	0.0201	0.6272	0.0393	-0.003	0.6	-0.0042	0.5719	94.6283	1.4269	-55.0026
11	0.3657	0.1836	0.3052	0.2804	0.097	0.2751	-0.0314	0.0932	0.0718	-0.0212	-0.0085	0.0198	-0.0224	0.0581	0.04	0.6478	0.0203	0.0227	0.5884	-0.0229	0.6812	-12.1823	-17.3113	-15.0041
12	0.9801	-0.279	-0.0417	0.7256	0.4392	0.5964	-0.0251	-0.0473	-0.0131	-0.1217	0.0041	0.1458	-0.0576	-0.1126	0.021	0.326	0.0112	0.0027	0.2752	0.0295	0.1095	47.5559	-13.0348	28.7471
13	0.2225	0.4719	0.167	1.0185	0.2326	1.1217	-0.03	-0.0134	0.0434	-0.0509	-0.0416	0.0903	-0.0367	-0.0811	0.0716	0.2691	0.0389	0.0164	0.2532	-0.0371	0.0707	61.6033	-51.5844	15.333
14	1.5528	0.4688	-0.0639	1.293	0.1354	1.5385	0.0302	-0.1622	0.0654	0.0293	-0.1426	0.1247	0.0375	-0.0975	0.1124	0.1301	-0.006	0.0054	0.1904	-0.0216	0.019	46.769	-84.3145	14.2735
15	0.9433	-0.1209	0.3791	0.9818	-0.0791	1.2343	0.0671	0.0314	0.0872	-0.1348	-0.1014	0.0902	-0.006	-0.0842	0.0343	0.2849	-0.0552	0.0358	0.3439	0.0085	0.1632	37.113	-32.951	70.0913
16	0.0398	-0.0358	0.1385	0.041	-0.1408	0.5224	0.0085	-0.055	0.0129	0.0113	-0.0173	-0.0092	0.0713	-0.0536	0.0088	0.6166	-0.0167	0.0073	0.5878	-0.0105	0.6134	2.9663	-14.2975	29.2439
17	0.7357	0.0707	-0.4045	0.7926	0.3265	1.4953	-0.0155	-0.002	-0.1018	-0.0085	0.0236	0.0192	0.0606	0.1265	-0.0081	0.232	-0.0144	-0.0052	0.2994	-0.0039	0.1322	73.5057	-29.8685	55.2581
18	0.4215	0.0174	0.4344	0.9139	0.0493	1.4197	-0.0144	-0.1174	0.073	0.0585	0.0142	-0.0735	0.0727	0.1347	0.0002	0.3188	0.0078	0.0091	0.2843	-0.0141	0.1005	3.7473	-83.7855	29.26
19	2.0334	0.1582	0.4335	1.1787	-0.682	1.9178	0.0045	0.0749	0.1956	-0.0914	-0.0881	-0.0044	-0.0741	0.1464	0.0836	0.1566	-0.0011	0.0242	0.1519	0.003	0.0247	34.9275	-104.0634	55.3356
20	0.6522	0.2367	-0.1229	0.9978	0.2054	1.3584	-0.0262	0.0837	-0.1004	-0.0412	0.0046	0.1237	-0.0425	0.0951	0.0217	0.2511	-0.0427	-0.0321	0.3517	-0.042	0.1624	16.6706	-62.3341	68.7042
21	1.0396	-0.2924	-0.0601	1.3207	-0.3455	1.295	0.0392	0.0117	0.0369	-0.0184	-0.075	0.0263	-0.059	-0.0557	0.0358	0.2447	-0.0218	0.0104	0.251	-0.0118	0.1261	95.0706	-70.1571	55.181
22	1.5384	0.1361	-0.5455	1.0597	0.0843	0.877	0.0179	-0.1082	-0.01	0.0367	-0.0254	0.0431	-0.0434	0.0613	0.0074	0.2921	-0.0007	0.003	0.2203	0.0165	0.1142	-12.0492	-51.3421	15.1556
23	0.4813	-0.3747	-0.1377	0.928	0.4126	1.107	-0.007	0.0421	-0.0382	0.0052	-0.0633	-0.004	0.068	-0.0538	0.0702	0.228	-0.0026	0.0243	0.3016	-0.0106	0.1613	74.698	27.2999	-69.1459
24	0.1442	0.1615	-0.0785	0.1907	-0.0853	0.0788	-0.0427	0.0568	0.0406	-0.0952	-0.0028	0.0555	-0.0987	0.0366	0.0455	0.6689	-0.0076	-0.0376	0.7169	0.0049	0.6585	73.8963	-96.2279	69.7133

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	196 - 493
2	X-RAY DIFFRACTION	2	B	196 - 493
3	X-RAY DIFFRACTION	3	C	196 - 493
4	X-RAY DIFFRACTION	4	D	196 - 493
5	X-RAY DIFFRACTION	5	E	196 - 493
6	X-RAY DIFFRACTION	6	F	196 - 493
7	X-RAY DIFFRACTION	7	G	196 - 493
8	X-RAY DIFFRACTION	8	H	196 - 493
9	X-RAY DIFFRACTION	9	I	196 - 493
10	X-RAY DIFFRACTION	10	J	196 - 493
11	X-RAY DIFFRACTION	11	K	196 - 493
12	X-RAY DIFFRACTION	12	L	196 - 493
13	X-RAY DIFFRACTION	13	M	196 - 493
14	X-RAY DIFFRACTION	14	N	196 - 493
15	X-RAY DIFFRACTION	15	O	196 - 493
16	X-RAY DIFFRACTION	16	P	196 - 493
17	X-RAY DIFFRACTION	17	Q	196 - 493
18	X-RAY DIFFRACTION	18	R	196 - 493
19	X-RAY DIFFRACTION	19	S	196 - 493
20	X-RAY DIFFRACTION	20	T	196 - 493
21	X-RAY DIFFRACTION	21	U	196 - 493
22	X-RAY DIFFRACTION	22	V	196 - 493
23	X-RAY DIFFRACTION	23	W	196 - 493
24	X-RAY DIFFRACTION	24	X	196 - 493