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- PDB-5mv4: ACC1 Fab fragment in complex with citrullinated CII616-639 epitop... -

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Basic information

Entry
Database: PDB / ID: 5mv4
TitleACC1 Fab fragment in complex with citrullinated CII616-639 epitope of collagen type II (ptm23)
Components
  • ACC1 antibody Fab fragment, heavy chain
  • ACC1 antibody Fab fragment, light chain
  • synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
KeywordsIMMUNE SYSTEM / anti-citrullinated protein antibody (ACPA) Fab fragment collagen type II citrullinated C1 epitope
Function / homology
Function and homology information


Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / anterior head development / MET activates PTK2 signaling ...Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / anterior head development / MET activates PTK2 signaling / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / embryonic skeletal joint morphogenesis / otic vesicle development / ECM proteoglycans / limb bud formation / Collagen chain trimerization / proteoglycan metabolic process / limb morphogenesis / platelet-derived growth factor binding / extracellular matrix structural constituent conferring tensile strength / Extracellular matrix organization / Integrin cell surface interactions / notochord development / cartilage development involved in endochondral bone morphogenesis / Collagen biosynthesis and modifying enzymes / MHC class II protein binding / cellular response to BMP stimulus / tissue homeostasis / Signaling by PDGF / endochondral ossification / collagen trimer / NCAM1 interactions / skeletal system morphogenesis / collagen fibril organization / cartilage development / proteoglycan binding / inner ear morphogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / cartilage condensation / roof of mouth development / inner ear development / Collagen degradation / Non-integrin membrane-ECM interactions / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ECM proteoglycans / Integrin cell surface interactions / chondrocyte differentiation / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / extracellular matrix / ossification / skeletal system development / central nervous system development / sensory perception of sound / bone development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of gene expression / collagen-containing extracellular matrix / endoplasmic reticulum lumen / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Collagen alpha-1(II) chain / Collagen alpha-1(II) chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDobritzsch, D. / Holmdahl, R. / Ge, C.
Funding support Sweden, 5items
OrganizationGrant numberCountry
Swedish Foundation for Strategic ResearchRBa08-0047 Sweden
Swedish Foundation for Strategic ResearchRB13-015 Sweden
Knut and Alice Wallenberg FoundationKAW 2010.0148 Sweden
Swedish Research CouncilK2011-52X-07931-25-5, 2015-02662, K2009-75SX-21029-01-3, K2012-75SX-22072-01-3 Sweden
European UnionIMI 115142
CitationJournal: JCI Insight / Year: 2017
Title: Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage.
Authors: Ge, C. / Tong, D. / Liang, B. / Lonnblom, E. / Schneider, N. / Hagert, C. / Viljanen, J. / Ayoglu, B. / Stawikowska, R. / Nilsson, P. / Fields, G.B. / Skogh, T. / Kastbom, A. / Kihlberg, J. ...Authors: Ge, C. / Tong, D. / Liang, B. / Lonnblom, E. / Schneider, N. / Hagert, C. / Viljanen, J. / Ayoglu, B. / Stawikowska, R. / Nilsson, P. / Fields, G.B. / Skogh, T. / Kastbom, A. / Kihlberg, J. / Burkhardt, H. / Dobritzsch, D. / Holmdahl, R.
History
DepositionJan 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACC1 antibody Fab fragment, heavy chain
B: ACC1 antibody Fab fragment, light chain
X: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
C: ACC1 antibody Fab fragment, heavy chain
D: ACC1 antibody Fab fragment, light chain
E: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
F: ACC1 antibody Fab fragment, heavy chain
G: ACC1 antibody Fab fragment, light chain
H: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
I: ACC1 antibody Fab fragment, heavy chain
J: ACC1 antibody Fab fragment, light chain
K: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
L: ACC1 antibody Fab fragment, heavy chain
M: ACC1 antibody Fab fragment, light chain
N: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
O: ACC1 antibody Fab fragment, heavy chain
P: ACC1 antibody Fab fragment, light chain
Q: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
R: ACC1 antibody Fab fragment, heavy chain
S: ACC1 antibody Fab fragment, light chain
T: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
U: ACC1 antibody Fab fragment, heavy chain
V: ACC1 antibody Fab fragment, light chain
W: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
hetero molecules


Theoretical massNumber of molelcules
Total (without water)410,47032
Polymers409,70124
Non-polymers7698
Water4,576254
1
A: ACC1 antibody Fab fragment, heavy chain
B: ACC1 antibody Fab fragment, light chain
X: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3094
Polymers51,2133
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-51 kcal/mol
Surface area19780 Å2
MethodPISA
2
C: ACC1 antibody Fab fragment, heavy chain
D: ACC1 antibody Fab fragment, light chain
E: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3094
Polymers51,2133
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-52 kcal/mol
Surface area19870 Å2
MethodPISA
3
F: ACC1 antibody Fab fragment, heavy chain
G: ACC1 antibody Fab fragment, light chain
H: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3094
Polymers51,2133
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-55 kcal/mol
Surface area19560 Å2
MethodPISA
4
I: ACC1 antibody Fab fragment, heavy chain
J: ACC1 antibody Fab fragment, light chain
K: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3094
Polymers51,2133
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-55 kcal/mol
Surface area19860 Å2
MethodPISA
5
L: ACC1 antibody Fab fragment, heavy chain
M: ACC1 antibody Fab fragment, light chain
N: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3094
Polymers51,2133
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-51 kcal/mol
Surface area19800 Å2
MethodPISA
6
O: ACC1 antibody Fab fragment, heavy chain
P: ACC1 antibody Fab fragment, light chain
Q: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3094
Polymers51,2133
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-54 kcal/mol
Surface area19910 Å2
MethodPISA
7
R: ACC1 antibody Fab fragment, heavy chain
S: ACC1 antibody Fab fragment, light chain
T: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3094
Polymers51,2133
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-55 kcal/mol
Surface area19880 Å2
MethodPISA
8
U: ACC1 antibody Fab fragment, heavy chain
V: ACC1 antibody Fab fragment, light chain
W: synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3094
Polymers51,2133
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-54 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.238, 91.601, 182.357
Angle α, β, γ (deg.)90.00, 91.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22F
13A
23I
14A
24L
15A
25O
16A
26R
17A
27U
18B
28D
19B
29G
110B
210J
111B
211M
112B
212P
113B
213S
114B
214V
115X
215E
116X
216H
117X
217K
118X
218N
119X
219Q
120X
220T
121X
221W
122C
222F
123C
223I
124C
224L
125C
225O
126C
226R
127C
227U
128D
228G
129D
229J
130D
230M
131D
231P
132D
232S
133D
233V
134E
234H
135E
235K
136E
236N
137E
237Q
138E
238T
139E
239W
140F
240I
141F
241L
142F
242O
143F
243R
144F
244U
145G
245J
146G
246M
147G
247P
148G
248S
149G
249V
150H
250K
151H
251N
152H
252Q
153H
253T
154H
254W
155I
255L
156I
256O
157I
257R
158I
258U
159J
259M
160J
260P
161J
261S
162J
262V
163K
263N
164K
264Q
165K
265T
166K
266W
167L
267O
168L
268R
169L
269U
170M
270P
171M
271S
172M
272V
173N
273Q
174N
274T
175N
275W
176O
276R
177O
277U
178P
278S
179P
279V
180Q
280T
181Q
281W
182R
282U
183S
283V
184T
284W

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPROAA1 - 2181 - 218
21GLUGLUPROPROCD1 - 2181 - 218
12GLUGLUPROPROAA1 - 2181 - 218
22GLUGLUPROPROFG1 - 2181 - 218
13GLUGLUPROPROAA1 - 2181 - 218
23GLUGLUPROPROIJ1 - 2181 - 218
14GLUGLUPROPROAA1 - 2181 - 218
24GLUGLUPROPROLM1 - 2181 - 218
15GLUGLUPROPROAA1 - 2181 - 218
25GLUGLUPROPROOP1 - 2181 - 218
16GLUGLUPROPROAA1 - 2181 - 218
26GLUGLUPROPRORS1 - 2181 - 218
17GLUGLUPROPROAA1 - 2181 - 218
27GLUGLUPROPROUV1 - 2181 - 218
18ASPASPGLUGLUBB1 - 2171 - 217
28ASPASPGLUGLUDE1 - 2171 - 217
19ASPASPASNASNBB1 - 2161 - 216
29ASPASPASNASNGH1 - 2161 - 216
110ASPASPASNASNBB1 - 2161 - 216
210ASPASPASNASNJK1 - 2161 - 216
111ASPASPGLUGLUBB1 - 2171 - 217
211ASPASPGLUGLUMN1 - 2171 - 217
112ASPASPASNASNBB1 - 2161 - 216
212ASPASPASNASNPQ1 - 2161 - 216
113ASPASPASNASNBB1 - 2161 - 216
213ASPASPASNASNST1 - 2161 - 216
114ASPASPASNASNBB1 - 2161 - 216
214ASPASPASNASNVW1 - 2161 - 216
115HYPHYPPROPROXC21 - 3221 - 32
215HYPHYPPROPROEF21 - 3221 - 32
116HYPHYPGLYGLYXC21 - 3121 - 31
216HYPHYPGLYGLYHI21 - 3121 - 31
117HYPHYPGLYGLYXC21 - 3121 - 31
217HYPHYPGLYGLYKL21 - 3121 - 31
118HYPHYPPROPROXC21 - 3221 - 32
218HYPHYPPROPRONO21 - 3221 - 32
119HYPHYPPROPROXC21 - 3221 - 32
219HYPHYPPROPROQR21 - 3221 - 32
120HYPHYPPROPROXC21 - 3221 - 32
220HYPHYPPROPROTU21 - 3221 - 32
121HYPHYPPROPROXC21 - 3221 - 32
221HYPHYPPROPROWX21 - 3221 - 32
122GLUGLUPROPROCD1 - 2181 - 218
222GLUGLUPROPROFG1 - 2181 - 218
123GLUGLUPROPROCD1 - 2181 - 218
223GLUGLUPROPROIJ1 - 2181 - 218
124GLUGLUPROPROCD1 - 2181 - 218
224GLUGLUPROPROLM1 - 2181 - 218
125GLUGLUPROPROCD1 - 2181 - 218
225GLUGLUPROPROOP1 - 2181 - 218
126GLUGLUPROPROCD1 - 2181 - 218
226GLUGLUPROPRORS1 - 2181 - 218
127GLUGLUPROPROCD1 - 2181 - 218
227GLUGLUPROPROUV1 - 2181 - 218
128ASPASPASNASNDE1 - 2161 - 216
228ASPASPASNASNGH1 - 2161 - 216
129ASPASPASNASNDE1 - 2161 - 216
229ASPASPASNASNJK1 - 2161 - 216
130ASPASPGLUGLUDE1 - 2171 - 217
230ASPASPGLUGLUMN1 - 2171 - 217
131ASPASPASNASNDE1 - 2161 - 216
231ASPASPASNASNPQ1 - 2161 - 216
132ASPASPASNASNDE1 - 2161 - 216
232ASPASPASNASNST1 - 2161 - 216
133ASPASPASNASNDE1 - 2161 - 216
233ASPASPASNASNVW1 - 2161 - 216
134HYPHYPGLYGLYEF21 - 3121 - 31
234HYPHYPGLYGLYHI21 - 3121 - 31
135HYPHYPGLYGLYEF21 - 3121 - 31
235HYPHYPGLYGLYKL21 - 3121 - 31
136HYPHYPPROPROEF21 - 3221 - 32
236HYPHYPPROPRONO21 - 3221 - 32
137HYPHYPPROPROEF21 - 3221 - 32
237HYPHYPPROPROQR21 - 3221 - 32
138HYPHYPPROPROEF21 - 3221 - 32
238HYPHYPPROPROTU21 - 3221 - 32
139HYPHYPPROPROEF21 - 3221 - 32
239HYPHYPPROPROWX21 - 3221 - 32
140GLUGLUPROPROFG1 - 2181 - 218
240GLUGLUPROPROIJ1 - 2181 - 218
141GLUGLUPROPROFG1 - 2181 - 218
241GLUGLUPROPROLM1 - 2181 - 218
142GLUGLUPROPROFG1 - 2181 - 218
242GLUGLUPROPROOP1 - 2181 - 218
143GLUGLUPROPROFG1 - 2181 - 218
243GLUGLUPROPRORS1 - 2181 - 218
144GLUGLUPROPROFG1 - 2181 - 218
244GLUGLUPROPROUV1 - 2181 - 218
145ASPASPCYSCYSGH1 - 2181 - 218
245ASPASPCYSCYSJK1 - 2181 - 218
146ASPASPASNASNGH1 - 2161 - 216
246ASPASPASNASNMN1 - 2161 - 216
147ASPASPCYSCYSGH1 - 2181 - 218
247ASPASPCYSCYSPQ1 - 2181 - 218
148ASPASPCYSCYSGH1 - 2181 - 218
248ASPASPCYSCYSST1 - 2181 - 218
149ASPASPCYSCYSGH1 - 2181 - 218
249ASPASPCYSCYSVW1 - 2181 - 218
150HYPHYPALAALAHI21 - 3321 - 33
250HYPHYPALAALAKL21 - 3321 - 33
151HYPHYPGLYGLYHI21 - 3121 - 31
251HYPHYPGLYGLYNO21 - 3121 - 31
152HYPHYPGLYGLYHI21 - 3121 - 31
252HYPHYPGLYGLYQR21 - 3121 - 31
153HYPHYPGLYGLYHI21 - 3121 - 31
253HYPHYPGLYGLYTU21 - 3121 - 31
154HYPHYPGLYGLYHI21 - 3121 - 31
254HYPHYPGLYGLYWX21 - 3121 - 31
155GLUGLUPROPROIJ1 - 2181 - 218
255GLUGLUPROPROLM1 - 2181 - 218
156GLUGLUPROPROIJ1 - 2181 - 218
256GLUGLUPROPROOP1 - 2181 - 218
157GLUGLUPROPROIJ1 - 2181 - 218
257GLUGLUPROPRORS1 - 2181 - 218
158GLUGLUPROPROIJ1 - 2181 - 218
258GLUGLUPROPROUV1 - 2181 - 218
159ASPASPASNASNJK1 - 2161 - 216
259ASPASPASNASNMN1 - 2161 - 216
160ASPASPCYSCYSJK1 - 2181 - 218
260ASPASPCYSCYSPQ1 - 2181 - 218
161ASPASPCYSCYSJK1 - 2181 - 218
261ASPASPCYSCYSST1 - 2181 - 218
162ASPASPCYSCYSJK1 - 2181 - 218
262ASPASPCYSCYSVW1 - 2181 - 218
163HYPHYPGLYGLYKL21 - 3121 - 31
263HYPHYPGLYGLYNO21 - 3121 - 31
164HYPHYPGLYGLYKL21 - 3121 - 31
264HYPHYPGLYGLYQR21 - 3121 - 31
165HYPHYPGLYGLYKL21 - 3121 - 31
265HYPHYPGLYGLYTU21 - 3121 - 31
166HYPHYPGLYGLYKL21 - 3121 - 31
266HYPHYPGLYGLYWX21 - 3121 - 31
167GLUGLUPROPROLM1 - 2181 - 218
267GLUGLUPROPROOP1 - 2181 - 218
168GLUGLUPROPROLM1 - 2181 - 218
268GLUGLUPROPRORS1 - 2181 - 218
169GLUGLUPROPROLM1 - 2181 - 218
269GLUGLUPROPROUV1 - 2181 - 218
170ASPASPASNASNMN1 - 2161 - 216
270ASPASPASNASNPQ1 - 2161 - 216
171ASPASPASNASNMN1 - 2161 - 216
271ASPASPASNASNST1 - 2161 - 216
172ASPASPASNASNMN1 - 2161 - 216
272ASPASPASNASNVW1 - 2161 - 216
173HYPHYPPROPRONO21 - 3221 - 32
273HYPHYPPROPROQR21 - 3221 - 32
174HYPHYPPROPRONO21 - 3221 - 32
274HYPHYPPROPROTU21 - 3221 - 32
175HYPHYPPROPRONO21 - 3221 - 32
275HYPHYPPROPROWX21 - 3221 - 32
176GLUGLUPROPROOP1 - 2181 - 218
276GLUGLUPROPRORS1 - 2181 - 218
177GLUGLUPROPROOP1 - 2181 - 218
277GLUGLUPROPROUV1 - 2181 - 218
178ASPASPCYSCYSPQ1 - 2181 - 218
278ASPASPCYSCYSST1 - 2181 - 218
179ASPASPCYSCYSPQ1 - 2181 - 218
279ASPASPCYSCYSVW1 - 2181 - 218
180HYPHYPPROPROQR21 - 3221 - 32
280HYPHYPPROPROTU21 - 3221 - 32
181HYPHYPPROPROQR21 - 3221 - 32
281HYPHYPPROPROWX21 - 3221 - 32
182GLUGLUPROPRORS1 - 2181 - 218
282GLUGLUPROPROUV1 - 2181 - 218
183ASPASPCYSCYSST1 - 2181 - 218
283ASPASPCYSCYSVW1 - 2181 - 218
184HYPHYPPROPROTU21 - 3221 - 32
284HYPHYPPROPROWX21 - 3221 - 32

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

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Components

#1: Antibody
ACC1 antibody Fab fragment, heavy chain


Mass: 23353.164 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: B cell hybridoma / Strain: B10.RIII.Cia5
#2: Antibody
ACC1 antibody Fab fragment, light chain


Mass: 23721.199 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: B cell hybridoma / Strain: B10.RIII.Cia5
#3: Protein/peptide
synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639 / Alpha-1 type II collagen


Mass: 4138.319 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: the synthesized peptide is (homo)trimeric and triple-helical in solution; one of the component single chains should contain the "lysine knot" sequence extension KKYG to promote chemical ...Details: the synthesized peptide is (homo)trimeric and triple-helical in solution; one of the component single chains should contain the "lysine knot" sequence extension KKYG to promote chemical crosslinking between the C-termini of the three chains; they are also biotinylated for purification purposes
Source: (synth.) Mus musculus (house mouse) / References: UniProt: P28481, UniProt: P02458*PLUS
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% (w/v) PEG 6000, 0.1 M MES pH 6.0, 0.2 M CaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.9→32.8 Å / Num. obs: 84765 / % possible obs: 97.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.182 / Net I/σ(I): 6.9
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4516 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MU0

5mu0


Resolution: 2.9→32.8 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.906 / SU B: 47.72 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.428
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS TLS refinement was used
RfactorNum. reflection% reflectionSelection details
Rfree0.24651 4191 4.9 %RANDOM
Rwork0.23234 ---
obs0.23305 80564 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.092 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å2-0.22 Å2
2---0.58 Å20 Å2
3---2.07 Å2
Refinement stepCycle: 1 / Resolution: 2.9→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27002 0 40 254 27296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227713
X-RAY DIFFRACTIONr_bond_other_d0.0020.0225196
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.94837681
X-RAY DIFFRACTIONr_angle_other_deg1.038358429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40553536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55524.5261096
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.096154357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.58515112
X-RAY DIFFRACTIONr_chiral_restr0.1010.24217
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02131224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026104
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1830.93214231
X-RAY DIFFRACTIONr_mcbond_other0.1830.93214230
X-RAY DIFFRACTIONr_mcangle_it0.3431.39617738
X-RAY DIFFRACTIONr_mcangle_other0.3431.39717739
X-RAY DIFFRACTIONr_scbond_it0.1660.94413482
X-RAY DIFFRACTIONr_scbond_other0.1190.93213451
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.2281.39319896
X-RAY DIFFRACTIONr_long_range_B_refined1.91510.42727790
X-RAY DIFFRACTIONr_long_range_B_other1.9110.4227779
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A130260.05
12C130260.05
21A127640.05
22F127640.05
31A129660.05
32I129660.05
41A128680.05
42L128680.05
51A128940.05
52O128940.05
61A127560.06
62R127560.06
71A127440.04
72U127440.04
81B131980.04
82D131980.04
91B130520.05
92G130520.05
101B131020.04
102J131020.04
111B130240.06
112M130240.06
121B129820.06
122P129820.06
131B130800.04
132S130800.04
141B130600.05
142V130600.05
151X4220.08
152E4220.08
161X3880.08
162H3880.08
171X3900.08
172K3900.08
181X4220.08
182N4220.08
191X4200.08
192Q4200.08
201X4160.08
202T4160.08
211X4180.08
212W4180.08
221C127860.04
222F127860.04
231C129680.05
232I129680.05
241C128860.05
242L128860.05
251C129520.04
252O129520.04
261C127600.06
262R127600.06
271C127400.04
272U127400.04
281D130920.04
282G130920.04
291D131280.04
292J131280.04
301D130800.05
302M130800.05
311D130100.06
312P130100.06
321D130880.04
322S130880.04
331D131080.04
332V131080.04
341E4040.01
342H4040.01
351E4060.01
352K4060.01
361E4360.01
362N4360.01
371E4340.01
372Q4340.01
381E4280.01
382T4280.01
391E4320.01
392W4320.01
401F128320.03
402I128320.03
411F127420.04
412L127420.04
421F128160.04
422O128160.04
431F126920.06
432R126920.06
441F127120.05
442U127120.05
451G132220.04
452J132220.04
461G130700.05
462M130700.05
471G131760.05
472P131760.05
481G132000.05
482S132000.05
491G132180.03
492V132180.03
501H4640.08
502K4640.08
511H4000.01
512N4000.01
521H3980.01
522Q3980.01
531H3960.01
532T3960.01
541H3980.01
542W3980.01
551I128580.05
552L128580.05
561I129020.04
562O129020.04
571I128380.05
572R128380.05
581I127560.04
582U127560.04
591J130280.05
592M130280.05
601J131340.05
602P131340.05
611J131740.04
612S131740.04
621J131800.05
622V131800.05
631K4040.01
632N4040.01
641K4020.01
642Q4020.01
651K3960.01
652T3960.01
661K4000.01
662W4000.01
671L129200.04
672O129200.04
681L127620.05
682R127620.05
691L127340.04
692U127340.04
701M130080.06
702P130080.06
711M130300.04
712S130300.04
721M130420.05
722V130420.05
731N4380.01
732Q4380.01
741N4280.01
742T4280.01
751N4320.01
752W4320.01
761O128060.06
762R128060.06
771O127800.04
772U127800.04
781P131160.05
782S131160.05
791P131320.06
792V131320.06
801Q4280.01
802T4280.01
811Q4320.01
812W4320.01
821R127000.05
822U127000.05
831S131960.04
832V131960.04
841T4280.01
842W4280.01
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 301 -
Rwork0.367 5922 -
obs--97.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
16.20050.8951.32444.18440.46390.746-0.01540.15650.3212-0.2382-0.0744-0.3377-0.18170.09830.08980.14190.02840.08680.2214-0.00340.338529.275225.217573.6027
24.738-1.7496-1.00026.27581.02123.5695-0.03260.51770.0718-0.2977-0.10550.01170.04010.24870.13810.164-0.0483-0.09130.365-0.03830.522659.902613.855572.2264
35.2373-2.10690.08035.51480.4691.4754-0.00960.3356-0.3244-0.07360.09540.03630.2516-0.1162-0.08570.0994-0.08010.03340.2585-0.05260.236525.78862.975777.9209
45.01542.8970.37272.63970.0211.28080.0751-0.2919-0.10090.1793-0.2189-0.00010.0830.19320.14380.14930.06390.04530.3087-0.07870.543261.93134.669584.9045
56.27511.0490.63190.48560.06660.2079-0.0035-0.43370.4460.0946-0.05560.1535-0.1203-0.05730.0590.231-0.01290.04330.3516-0.02670.332284.5783-18.489917.7133
63.74531.0266-0.35456.7952-1.12763.3090.0515-0.4175-0.00180.2977-0.0149-0.05510.0586-0.2489-0.03660.1839-0.0057-0.13150.40620.02220.404357.2961-29.451419.691
74.76021.58-0.05614.92020.10851.34420.0336-0.4753-0.40580.1306-0.0051-0.09550.25830.0815-0.02850.10830.05590.01170.32630.11340.264691.3449-39.96313.5414
85.1375-3.36740.56993.801-0.81821.88040.17680.2885-0.0889-0.2194-0.2438-0.05150.1038-0.07890.0670.0971-0.07320.02990.3090.0380.423955.5284-38.4146.6369
93.1913-1.3316-1.96541.50041.01763.06120.11130.3560.0948-0.183-0.04690.2207-0.2464-0.2361-0.06430.0925-0.0473-0.02140.30680.19110.4635105.82720.550983.1264
102.52920.28860.67381.92321.50415.93540.1988-0.18840.20820.0140.09980.0348-0.7954-0.2041-0.29870.29070.10250.1840.41970.1130.591994.673916.3589102.754
112.6693-0.7089-0.79293.2819-0.40135.6758-0.08-0.27330.05390.1590.0289-0.34940.29790.51110.05110.0398-0.0203-0.00860.26540.07220.4687111.9035-14.278799.2624
124.7551-4.05761.04144.9054-1.08521.2585-0.1484-0.5344-0.50770.46560.380.6652-0.2289-0.8299-0.23160.31560.02260.15980.80310.17740.667385.04337.2934112.3106
133.9099-2.1289-0.20792.0152-0.08343.7338-0.01660.1870.184-0.09540.03430.138-0.1599-0.0536-0.01760.0837-0.03740.00390.311-0.00940.337110.32451.5885-9.8675
142.54470.12581.06863.03221.20296.4730.0701-0.02980.13090.09480.0585-0.1335-0.5204-0.2843-0.12860.15890.03740.08710.37620.07920.435396.604520.197212.5329
151.0758-1.1623-0.80823.04750.92562.2281-0.0261-0.1975-0.01390.19710.1337-0.2610.27070.3053-0.10750.0639-0.0359-0.01510.3822-0.03820.421109.847-6.474510.9882
165.483-3.25511.03513.0969-0.19791.71240.0946-0.2432-0.2249-0.04770.00380.3427-0.0413-0.4704-0.09840.2091-0.06230.05880.550.01810.400386.064111.052822.2315
171.7328-1.95780.73263.7171-0.81644.11-0.0795-0.0416-0.14550.1250.09970.21380.1071-0.4676-0.02020.086-0.05730.01960.2779-0.02960.4271.2166-44.348881.2306
184.69831.03296.97230.24821.505110.398-0.276-0.21330.1132-0.00520.1176-0.0314-0.5404-0.53270.15830.8520.0922-0.03251.3294-0.21540.815855.5617-32.832542.9725
190.67310.39821.94241.02180.56336.9968-0.1001-0.00540.0508-0.44950.04410.3708-0.1055-1.10490.05590.35320.064-0.03881.1752-0.22750.857356.2183-36.10655.2886
202.8981.68750.6712.22022.00068.0467-0.01610.02870.0752-0.0473-0.1436-0.19970.4961.27160.15970.20810.1020.08130.4360.02690.537192.6611-45.334466.4025
212.2523-1.06330.34172.71320.14.5860.0930.1751-0.29-0.36220.0199-0.05940.61780.0233-0.11290.2481-0.04670.04340.2163-0.05730.419483.6629-47.803262.2989
223.0719-1.39850.59994.7031-0.01530.19710.2287-0.25690.9231-1.0192-0.38940.1599-0.1527-0.31270.16081.05310.32750.03121.07410.00410.702465.6291-24.368447.5013
233.8802-2.1680.9892.7137-1.18510.5850.0030.45841.1524-0.4147-0.00210.10180.0216-0.2246-0.00091.03310.253-0.03250.98120.09080.815666.4698-25.2845.9529
242.76351.8883-0.06076.06020.743.5424-0.13350.0544-0.1511-0.15530.1561-0.14580.03340.2837-0.02260.06240.04130.00050.29380.00320.360245.1533.72048.8396
250.24290.3491-1.41360.6436-2.24068.6711-0.0041-0.0420.0880.14080.1487-0.03030.0517-0.1074-0.14460.60920.0107-0.01830.77260.01390.542363.023515.026441.0416
261.1944-0.08131.13312.4893-0.38216.558-0.0825-0.5267-0.02850.49380.0694-0.3617-0.20680.55760.01320.35230.01380.00360.72910.04540.618861.210911.344134.7919
272.8978-0.33530.07413.3392-0.66856.38370.0252-0.2026-0.22860.3260.14730.33160.629-0.6179-0.17240.27430.00840.06560.2590.06520.468329.29320.280925.2374
284.77511.4601-0.1251.02410.23380.78920.2257-0.79921.08880.4315-0.0410.0352-0.55890.3386-0.18471.1251-0.01990.02960.9154-0.21190.682352.367621.981344.5869
293.8813-0.33670.46846.10130.44391.5309-0.1220.1875-0.0188-0.32460.10870.1986-0.0938-0.21780.01330.219-0.04150.0830.3240.03930.465892.256-23.894552.9929
305.07010.28260.17353.8622-0.09722.9139-0.19410.02310.3853-0.03910.15180.1123-0.5255-0.13490.04230.48980.06130.02420.2901-0.030.542298.13537.160246.7667
313.66540.906-0.01163.71290.56392.91160.0810.2408-0.5939-0.0939-0.042-0.6940.0770.4584-0.0390.22990.0520.09120.33490.04130.5704113.0816-21.755961.9857
325.3522-3.86621.29874.7726-1.3271.1268-0.5055-0.60310.45590.4130.2295-0.186-0.7234-0.32080.2760.85340.0652-0.05970.4555-0.07220.5745104.185914.10559.9059
332.9943-0.4347-0.13616.3941-0.03320.3487-0.5269-0.70550.40720.64530.4875-0.53810.04580.19230.03940.4560.2214-0.01020.6151-0.08860.4694144.915-63.303937.4519
3495.6895-8.056410.0482.0645-2.51933.07810.2131.0333-0.05530.14530.13410.2596-0.1328-0.1511-0.3470.72110.163-0.06740.7457-0.18971.0321128.9611-27.955744.8296
352.52410.40520.50093.44390.23881.4878-0.1061-0.77550.47550.32420.354-0.5289-0.3220.4818-0.24790.49240.1348-0.15670.8611-0.44791.5956139.9535-36.624143.2075
365.5286-3.3838-0.09875.65050.33241.8773-0.2179-0.3062-0.67950.40130.14010.81130.2139-0.26760.07780.2952-0.01990.08850.38950.00260.4592123.0393-62.711529.0374
372.09292.868-2.41054.2516-3.11773.03440.19150.27130.95960.20130.71050.9969-0.6032-0.0077-0.9020.8454-0.0251-0.2820.70430.03052.1285134.9135-27.762730.7828
384.39296.73140.179210.36230.27840.1024-0.0405-0.03220.1293-0.02360.0065-0.0353-0.21620.20270.0340.8623-0.085-0.14330.81010.00161.2608136.743-29.974629.659
392.81762.898-2.52425.2296-0.22574.98580.3759-0.4209-0.73760.457-0.2381-1.2961-0.36830.2157-0.13781.06510.2412-0.21220.76420.03691.6653128.2841-22.205629.469
401.8405-2.66032.36927.5132-0.84234.9435-0.0365-0.09550.0069-0.6543-0.33720.3376-0.5011-0.62380.37380.3246-0.0736-0.04760.5748-0.08980.461714.491513.741468.7826
4111.8636-2.53613.76546.9128-0.15552.4365-0.1232-0.5115-0.4290.13040.0286-0.3186-0.39030.52840.09460.3911-0.0208-0.1590.58990.10150.374102.5356-29.258122.4334
422.1882-4.4985-6.44079.253413.241918.9602-0.1681-0.24610.10870.36140.4851-0.28120.54340.731-0.3170.32110.06230.10040.59830.19260.7041124.3695-9.335685.8374
434.3947-3.61862.71982.9823-2.23831.69420.1323-0.0514-0.3629-0.08570.06070.27340.08370.0572-0.1930.306-0.00790.08790.74840.11180.7076122.4268-16.294884.7609
442.23210.6976-7.598.8480.275226.6509-0.2085-0.2458-0.1870.1151-0.2743-0.95510.72470.74890.48290.23350.0767-0.02570.5310.06110.7239126.6058-6.4309-5.1309
4521.2337-10.5872-4.672816.63896.61072.8902-0.1588-0.4787-1.15310.87040.3755-0.10370.60840.2745-0.21670.49430.07-0.09020.51280.02780.6309124.6396-13.2255-6.4076
461.8052-0.70971.34721.99441.88124.5726-0.04650.244-0.29750.83350.33-0.17061.12250.9773-0.28340.64950.1411-0.02590.43480.21470.789486.2032-57.888381.858
470.07980.0145-0.44460.2276-2.212523.14420.0545-0.0803-0.2691-0.21230.12730.15311.6279-1.6117-0.18180.6629-0.3218-0.23520.73210.04551.462330.8351-9.11699.059
484.3665-0.3268-0.60238.87373.9821.84960.08080.2146-0.08650.0749-0.0778-0.25140.0835-0.0409-0.0030.62610.06890.10240.47560.04560.6608106.3813-36.465453.8553
496.3052.6228-2.7452.514-1.53641.32010.1483-0.2088-0.19510.1099-0.20310.26660.01580.09750.05480.7861-0.04660.07230.62710.05490.6603130.3934-78.95437.2987
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2A120 - 218
3X-RAY DIFFRACTION3B1 - 108
4X-RAY DIFFRACTION4B109 - 217
5X-RAY DIFFRACTION5C1 - 131
6X-RAY DIFFRACTION6C132 - 218
7X-RAY DIFFRACTION7D1 - 106
8X-RAY DIFFRACTION8D107 - 217
9X-RAY DIFFRACTION9F1 - 138
10X-RAY DIFFRACTION10F139 - 218
11X-RAY DIFFRACTION11G1 - 106
12X-RAY DIFFRACTION12G107 - 218
13X-RAY DIFFRACTION13I1 - 117
14X-RAY DIFFRACTION14I118 - 218
15X-RAY DIFFRACTION15J1 - 134
16X-RAY DIFFRACTION16J135 - 218
17X-RAY DIFFRACTION17L1 - 124
18X-RAY DIFFRACTION18L125 - 142
19X-RAY DIFFRACTION19L143 - 218
20X-RAY DIFFRACTION20M1 - 34
21X-RAY DIFFRACTION21M35 - 123
22X-RAY DIFFRACTION22M124 - 160
23X-RAY DIFFRACTION23M161 - 217
24X-RAY DIFFRACTION24O1 - 118
25X-RAY DIFFRACTION25O119 - 141
26X-RAY DIFFRACTION26O142 - 218
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