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- PDB-5kj7: Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long u... -

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Basic information

Entry
Database: PDB / ID: 5kj7
TitleStructure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from XFEL diffraction
Components
  • (Synaptosomal-associated protein ...) x 2
  • Synaptotagmin-1
  • Syntaxin-1A
  • Vesicle-associated membrane protein 3
KeywordsENDOCYTOSIS / EXOCYTOSIS / XFEL STRUCTURE / SYNAPTIC FUSION COMPLEX / SYNAPTOTAGMIN1 / NEURONAL SNARE COMPLEX
Function / homology
Function and homology information


negative regulation of secretion by cell / RHOF GTPase cycle / RHOB GTPase cycle / RHOD GTPase cycle / ER-Phagosome pathway / RAC2 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / Retrograde transport at the Trans-Golgi-Network / RHOQ GTPase cycle ...negative regulation of secretion by cell / RHOF GTPase cycle / RHOB GTPase cycle / RHOD GTPase cycle / ER-Phagosome pathway / RAC2 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / Retrograde transport at the Trans-Golgi-Network / RHOQ GTPase cycle / RAC1 GTPase cycle / BLOC-1 complex / regulation of vesicle fusion / myosin head/neck binding / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / RHOA GTPase cycle / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / regulation of regulated secretory pathway / calcium ion-regulated exocytosis of neurotransmitter / spontaneous neurotransmitter secretion / positive regulation of vesicle fusion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / calcium-dependent activation of synaptic vesicle fusion / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / regulated exocytosis / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / extrinsic component of presynaptic membrane / dense core granule / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / synaptic vesicle docking / regulation of synaptic vesicle priming / regulation of establishment of protein localization / ribbon synapse / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / response to gravity / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / positive regulation of calcium ion-dependent exocytosis / vesicle docking / exocytic vesicle / regulation of exocytosis / secretion by cell / SNAP receptor activity / SNARE complex / chloride channel inhibitor activity / vesicle organization / protein heterooligomerization / clathrin-coated vesicle membrane / vesicle fusion / positive regulation of dopamine secretion / calcium-ion regulated exocytosis / Cargo recognition for clathrin-mediated endocytosis / LGI-ADAM interactions / Clathrin-mediated endocytosis / actomyosin / hormone secretion / Golgi to plasma membrane protein transport / positive regulation of dendrite extension / positive regulation of hormone secretion / neurotransmitter secretion / ATP-dependent protein binding / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / retrograde transport, endosome to Golgi / protein localization to membrane / syntaxin binding / syntaxin-1 binding / clathrin-coated vesicle / insulin secretion / endosomal transport / Neutrophil degranulation / SNARE complex assembly / positive regulation of neurotransmitter secretion / clathrin binding / neurotransmitter transport / low-density lipoprotein particle receptor binding / synaptic vesicle priming / regulation of synapse assembly / regulation of synaptic vesicle exocytosis / phosphatidylserine binding / myosin binding / positive regulation of receptor recycling / regulation of neuron projection development / intracellular vesicle / regulation of dopamine secretion / exocytosis
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / SNAP-25 domain / SNAP-25 family / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain ...Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / SNAP-25 domain / SNAP-25 family / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Synaptobrevin-like / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / SNARE / Synaptotagmin / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Synaptotagmin-1 / Syntaxin-1A / Synaptosomal-associated protein 25 / Vesicle-associated membrane protein 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsLyubimov, A.Y. / Uervirojnangkoorn, M. / Zhou, Q. / Zhao, M. / Sauter, N.K. / Brewster, A.S. / Weis, W.I. / Brunger, A.T.
Funding support United States, 3items
OrganizationGrant numberCountry
Hughes Collaborative Innovation Award United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102520 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM117126 United States
CitationJournal: Elife / Year: 2016
Title: Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex.
Authors: Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Zhou, Q. / Zhao, M. / Brewster, A.S. / Michels-Clark, T. / Holton, J.M. / Sauter, N.K. / Weis, W.I. / Brunger, A.T.
History
DepositionJun 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Nov 28, 2018Group: Data collection
Category: diffrn / pdbx_serial_crystallography_data_reduction ...diffrn / pdbx_serial_crystallography_data_reduction / pdbx_serial_crystallography_measurement / pdbx_serial_crystallography_sample_delivery_fixed_target
Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: Vesicle-associated membrane protein 3
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Synaptotagmin-1
F: Synaptotagmin-1
G: Vesicle-associated membrane protein 3
H: Syntaxin-1A
I: Synaptosomal-associated protein 25
J: Synaptosomal-associated protein 25
K: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,76730
Polymers158,00611
Non-polymers76119
Water30617
1
A: Vesicle-associated membrane protein 3
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,40915
Polymers63,0095
Non-polymers40110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1495
Polymers31,9891
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Vesicle-associated membrane protein 3
H: Syntaxin-1A
I: Synaptosomal-associated protein 25
J: Synaptosomal-associated protein 25
K: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,20910
Polymers63,0095
Non-polymers2005
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.386, 170.676, 291.014
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain E and (resseq 143:172 or (resid 173 and (name...
21(chain K and (resseq 143:172 or (resid 173 and (name...
12(chain A and (resseq 27:29 or (resid 30 and (name...
22(chain G and (resseq 27:32 or (resid 33 and (name...
13(chain C and (resseq 11:12 or (resid 13 and (name...
23(chain I and (resseq 11:58 or resseq 60:78 or (resid...
14(chain B and (resseq 191:197 or (resid 198 and (name...
24(chain H and (resseq 191:209 or resseq 211:227 or (resid...
15(chain D and (resseq 144:160 or (resid 161 and (name...
25(chain J and (resseq 144:161 or resseq 163:190 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYASPASP(chain E and (resseq 143:172 or (resid 173 and (name...EE143 - 1723 - 32
121METMETMETMET(chain E and (resseq 143:172 or (resid 173 and (name...EE17333
131LYSLYSVALVAL(chain E and (resseq 143:172 or (resid 173 and (name...EE141 - 4191 - 279
141LYSLYSVALVAL(chain E and (resseq 143:172 or (resid 173 and (name...EE141 - 4191 - 279
211GLYGLYASPASP(chain K and (resseq 143:172 or (resid 173 and (name...KK143 - 1723 - 32
221METMETMETMET(chain K and (resseq 143:172 or (resid 173 and (name...KK17333
231LYSLYSVALVAL(chain K and (resseq 143:172 or (resid 173 and (name...KK141 - 4191 - 279
241LYSLYSVALVAL(chain K and (resseq 143:172 or (resid 173 and (name...KK141 - 4191 - 279
112GLYGLYASNASN(chain A and (resseq 27:29 or (resid 30 and (name...AA27 - 291 - 3
122ARGARGARGARG(chain A and (resseq 27:29 or (resid 30 and (name...AA304
132GLYGLYTRPTRP(chain A and (resseq 27:29 or (resid 30 and (name...AA27 - 891 - 63
142GLYGLYTRPTRP(chain A and (resseq 27:29 or (resid 30 and (name...AA27 - 891 - 63
152GLYGLYTRPTRP(chain A and (resseq 27:29 or (resid 30 and (name...AA27 - 891 - 63
162GLYGLYTRPTRP(chain A and (resseq 27:29 or (resid 30 and (name...AA27 - 891 - 63
212GLYGLYLEULEU(chain G and (resseq 27:32 or (resid 33 and (name...GG27 - 321 - 6
222GLNGLNGLNGLN(chain G and (resseq 27:32 or (resid 33 and (name...GG337
232GLYGLYTRPTRP(chain G and (resseq 27:32 or (resid 33 and (name...GG27 - 891 - 63
242GLYGLYTRPTRP(chain G and (resseq 27:32 or (resid 33 and (name...GG27 - 891 - 63
252GLYGLYTRPTRP(chain G and (resseq 27:32 or (resid 33 and (name...GG27 - 891 - 63
113LEULEUGLUGLU(chain C and (resseq 11:12 or (resid 13 and (name...CC11 - 123 - 4
123GLUGLUGLUGLU(chain C and (resseq 11:12 or (resid 13 and (name...CC135
133ASNASNGLYGLY(chain C and (resseq 11:12 or (resid 13 and (name...CC9 - 821 - 74
143ASNASNGLYGLY(chain C and (resseq 11:12 or (resid 13 and (name...CC9 - 821 - 74
153ASNASNGLYGLY(chain C and (resseq 11:12 or (resid 13 and (name...CC9 - 821 - 74
213LEULEUASPASP(chain I and (resseq 11:58 or resseq 60:78 or (resid...II11 - 583 - 50
223VALVALLEULEU(chain I and (resseq 11:58 or resseq 60:78 or (resid...II60 - 7852 - 70
233LYSLYSLYSLYS(chain I and (resseq 11:58 or resseq 60:78 or (resid...II7971
243GLUGLULYSLYS(chain I and (resseq 11:58 or resseq 60:78 or (resid...II10 - 832 - 75
253GLUGLULYSLYS(chain I and (resseq 11:58 or resseq 60:78 or (resid...II10 - 832 - 75
263GLUGLULYSLYS(chain I and (resseq 11:58 or resseq 60:78 or (resid...II10 - 832 - 75
114ALAALATHRTHR(chain B and (resseq 191:197 or (resid 198 and (name...BB191 - 1971 - 7
124ARGARGARGARG(chain B and (resseq 191:197 or (resid 198 and (name...BB1988
134ALAALALYSLYS(chain B and (resseq 191:197 or (resid 198 and (name...BB191 - 2561 - 66
144ALAALALYSLYS(chain B and (resseq 191:197 or (resid 198 and (name...BB191 - 2561 - 66
154ALAALALYSLYS(chain B and (resseq 191:197 or (resid 198 and (name...BB191 - 2561 - 66
164ALAALALYSLYS(chain B and (resseq 191:197 or (resid 198 and (name...BB191 - 2561 - 66
214ALAALAILEILE(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2091 - 19
224GLUGLUGLYGLY(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH211 - 22721 - 37
234GLUGLUGLUGLU(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH22838
244ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
254ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
264ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
274ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
284ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
294ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
2104ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
115ASNASNLEULEU(chain D and (resseq 144:160 or (resid 161 and (name...DD144 - 1604 - 20
125ARGARGARGARG(chain D and (resseq 144:160 or (resid 161 and (name...DD16121
135ALAALAGLYGLY(chain D and (resseq 144:160 or (resid 161 and (name...DD141 - 2041 - 64
145ALAALAGLYGLY(chain D and (resseq 144:160 or (resid 161 and (name...DD141 - 2041 - 64
155ALAALAGLYGLY(chain D and (resseq 144:160 or (resid 161 and (name...DD141 - 2041 - 64
215ASNASNARGARG(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ144 - 1614 - 21
225METMETTHRTHR(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ163 - 19023 - 50
235ILEILEASNASN(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ192 - 19652 - 56
245GLNGLNGLNGLN(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ19757
255ALAALALEULEU(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ141 - 2031 - 63
265ALAALALEULEU(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ141 - 2031 - 63
275ALAALALEULEU(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ141 - 2031 - 63

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 3 types, 7 molecules AGBHEFK

#1: Protein Vesicle-associated membrane protein 3 / VAMP-3 / Cellubrevin / CEB / Synaptobrevin-3


Mass: 7231.061 Da / Num. of mol.: 2 / Fragment: UNP residues 14-76
Source method: isolated from a genetically manipulated source
Details: 96% helical (1 helices; 61 residues) / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp3, Syb3 / Production host: Escherichia coli (E. coli) / References: UniProt: P63025
#2: Protein Syntaxin-1A / Neuron-specific antigen HPC-1 / Synaptotagmin-associated 35 kDa protein / P35A


Mass: 7706.761 Da / Num. of mol.: 2 / Fragment: UNP residues 191-256
Source method: isolated from a genetically manipulated source
Details: 91% helical (1 helices; 61 residues) / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Production host: Escherichia coli (E. coli) / References: UniProt: P32851
#5: Protein Synaptotagmin-1 / Synaptotagmin I / SytI / p65


Mass: 31988.838 Da / Num. of mol.: 3 / Fragment: UNP residues 141-419
Source method: isolated from a genetically manipulated source
Details: 9% helical (5 helices; 27 residues) 45% beta sheet (19 strands; 129 residues)
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21707

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Synaptosomal-associated protein ... , 2 types, 4 molecules CIDJ

#3: Protein Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 8741.725 Da / Num. of mol.: 2 / Fragment: UNP residues 9-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli (E. coli) / References: UniProt: P60881
#4: Protein Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 7340.173 Da / Num. of mol.: 2 / Fragment: UNP residues 141- 204
Source method: isolated from a genetically manipulated source
Details: 92% helical (1 helices; 60 residues) / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli (E. coli) / References: UniProt: P60881

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Non-polymers , 2 types, 36 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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

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Sample preparation

CrystalDensity Matthews: 5.45 Å3/Da / Density % sol: 77.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.307 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: May 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.307 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 43622 / % possible obs: 97.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 66.8 Å2 / CC1/2: 0.943 / Rmerge(I) obs: 0.494 / Net I/σ(I): 3.6
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 0.2 / % possible all: 89.2
Serial crystallography measurementFocal spot size: 30 µm2 / Photons per pulse: 1 Tphotons/pulse / Pulse duration: 40 fsec. / Pulse photon energy: 9 keV
Serial crystallography sample delivery fixed targetMotion control: DCSS / Sample holding: cryo-loop
Sample solvent: 100 mM Tris-HCl (pH 8.5), 1.5 M ammonium sulfate
Support base: goniometer
Serial crystallography data reductionCrystal hits: 578 / Frames indexed: 309 / Frames total: 799

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.2data extraction
cctbx.xfeldata reduction
cctbx.primedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N7S, 3F04, 1UOW

1n7s

3f04

1uow


Resolution: 3.5→19.956 Å / SU ML: 0.86 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.2
RfactorNum. reflection% reflection
Rfree0.3291 2083 5.14 %
Rwork0.292 --
obs0.2939 40510 91.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 240.46 Å2 / Biso mean: 106 Å2 / Biso min: 26.94 Å2
Refinement stepCycle: final / Resolution: 3.5→19.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10542 0 19 17 10578
Biso mean--87.67 44.31 -
Num. residues----1365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210701
X-RAY DIFFRACTIONf_angle_d0.4514435
X-RAY DIFFRACTIONf_chiral_restr0.0371596
X-RAY DIFFRACTIONf_plane_restr0.0031919
X-RAY DIFFRACTIONf_dihedral_angle_d13.9416431
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11E2310X-RAY DIFFRACTION7.588TORSIONAL
12K2310X-RAY DIFFRACTION7.588TORSIONAL
21A572X-RAY DIFFRACTION7.588TORSIONAL
22G572X-RAY DIFFRACTION7.588TORSIONAL
31C596X-RAY DIFFRACTION7.588TORSIONAL
32I596X-RAY DIFFRACTION7.588TORSIONAL
41B538X-RAY DIFFRACTION7.588TORSIONAL
42H538X-RAY DIFFRACTION7.588TORSIONAL
51D508X-RAY DIFFRACTION7.588TORSIONAL
52J508X-RAY DIFFRACTION7.588TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5001-3.5810.4616530.391891096333
3.581-3.67010.44191140.3912033214773
3.6701-3.76860.37521140.3872199231380
3.7686-3.87880.40871430.37662683282695
3.8788-4.0030.43051440.36432651279597
4.003-4.14480.33651480.34732726287498
4.1448-4.30920.40091480.32912737288598
4.3092-4.50320.39511460.32012723286998
4.5032-4.73760.33281510.29992759291099
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6.7729-8.42490.2881560.25312864302099
8.4249-19.95640.21941610.216829813142100

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