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- PDB-9aw3: Yeast 20S proteasome soaked with MA9 crude extract -

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Basic information

Entry
Database: PDB / ID: 9aw3
TitleYeast 20S proteasome soaked with MA9 crude extract
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 3
  • (proteasome endopeptidase ...) x 2
  • PRE10 isoform 1
  • PRE7 isoform 1
  • Proteasome subunit beta
KeywordsHYDROLASE
Function / homology
Function and homology information


proteasome core complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 ...proteasome core complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / proteasome endopeptidase complex / endopeptidase activator activity / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / Neutrophil degranulation / proteasome complex / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / endoplasmic reticulum membrane / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site ...Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
PRE7 isoform 1 / proteasome endopeptidase complex / PRE10 isoform 1 / proteasome endopeptidase complex / Proteasome subunit beta / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-3 ...PRE7 isoform 1 / proteasome endopeptidase complex / PRE10 isoform 1 / proteasome endopeptidase complex / Proteasome subunit beta / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-3 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsMeneghello, R. / Rustiguel, J.K. / Fernandes, A.Z.N. / Trivella, D.B.B.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Other private1709-19681 Brazil
Sao Paulo Research Foundation (FAPESP)2014/10753-9 Brazil
Sao Paulo Research Foundation (FAPESP)2019/17721-9 Brazil
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: High-throughput protein crystallography to empower natural product-based drug discovery.
Authors: Meneghello, R. / Rustiguel, J.K. / de Araujo, E.A. / de Felicio, R. / Fernandes, A.Z.N. / Ferreira, E.L.F. / Gubiani, J.R. / Takeda, A.A.S. / Araujo, A. / de Lima Silva, C.C. / Bertonha, A.F. ...Authors: Meneghello, R. / Rustiguel, J.K. / de Araujo, E.A. / de Felicio, R. / Fernandes, A.Z.N. / Ferreira, E.L.F. / Gubiani, J.R. / Takeda, A.A.S. / Araujo, A. / de Lima Silva, C.C. / Bertonha, A.F. / Urano, R.P.M. / Trindade, D.M. / Cunha, T.M. / Cardoso, A.C. / Berlinck, R.G.S. / Nascimento, A.F.Z. / Trivella, D.B.B.
History
DepositionMar 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 7, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-3
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-6
F: PRE10 isoform 1
G: Proteasome subunit alpha type-1
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-3
Q: Proteasome subunit alpha type-4
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-6
T: PRE10 isoform 1
U: Proteasome subunit alpha type-1
H: proteasome endopeptidase complex
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-4
K: proteasome endopeptidase complex
L: PRE7 isoform 1
M: Proteasome subunit beta
N: Proteasome subunit beta type-1
V: proteasome endopeptidase complex
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-4
Y: proteasome endopeptidase complex
Z: PRE7 isoform 1
a: Proteasome subunit beta
b: Proteasome subunit beta type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)728,73638
Polymers728,27828
Non-polymers45810
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.964, 301.458, 142.649
Angle α, β, γ (deg.)90.000, 111.976, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "O" and (resid 3 through 60 or (resid 61...
d_1ens_2chain "B"
d_2ens_2(chain "P" and (resid 1 through 2 or (resid 3...
d_1ens_3(chain "C" and (resid 1 through 132 or (resid 133...
d_2ens_3(chain "Q" and (resid 1 through 46 or resid 50 through 241))
d_1ens_4(chain "D" and (resid 3 through 43 or (resid 44...
d_2ens_4(chain "R" and resid 3 through 242)
d_1ens_5chain "E"
d_2ens_5(chain "S" and (resid 3 through 48 or (resid 49...
d_1ens_6(chain "F" and (resid 1 through 200 or (resid 201...
d_2ens_6(chain "T" and resid 1 through 244)
d_1ens_7(chain "G" and (resid 2 through 67 or (resid 68...
d_2ens_7(chain "U" and (resid 2 through 38 or (resid 39...
d_1ens_8(chain "H" and (resid 1 through 28 or (resid 29...
d_2ens_8chain "V"
d_1ens_9chain "I"
d_2ens_9(chain "W" and (resid 1 through 16 or (resid 17...
d_1ens_10(chain "J" and (resid 1 through 109 or (resid 110...
d_2ens_10chain "X"
d_1ens_11chain "K"
d_2ens_11chain "Y"
d_1ens_12(chain "L" and (resid 1 through 160 or (resid 161...
d_2ens_12chain "Z"
d_1ens_13(chain "M" and (resid 1 through 224 or (resid 225...
d_2ens_13chain "a"
d_1ens_14(chain "N" and (resid 1 through 35 or (resid 36...
d_2ens_14chain "b"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASPASPLEULEUAA3 - 2503 - 250
d_21ens_1ASPASPLEULEUOH3 - 2503 - 250
d_11ens_2GLYGLYLYSLYSBB1 - 2462 - 247
d_21ens_2GLYGLYLYSLYSPI1 - 2172 - 218
d_22ens_2ASPASPLYSLYSPI221 - 246222 - 247
d_11ens_3GLYGLYGLNGLNCC1 - 2413 - 243
d_21ens_3GLYGLYARGARGQJ1 - 463 - 48
d_22ens_3LEULEUGLNGLNQJ50 - 24152 - 243
d_11ens_4GLYGLYGLUGLUDD3 - 24211 - 250
d_21ens_4GLYGLYGLUGLURK3 - 24211 - 250
d_11ens_5ASNASNILEILEEE3 - 2334 - 234
d_21ens_5ASNASNILEILESL3 - 2334 - 234
d_11ens_6GLYGLYASNASNFF1 - 2444 - 247
d_21ens_6GLYGLYASNASNTM1 - 2444 - 247
d_11ens_7GLYGLYASPASPGG2 - 24311 - 252
d_21ens_7GLYGLYASPASPUN2 - 24311 - 252
d_11ens_8THRTHRCYSCYSHO1 - 2211 - 221
d_21ens_8THRTHRCYSCYSVV1 - 2211 - 221
d_11ens_9SERSERASPASPIP1 - 2042 - 205
d_21ens_9SERSERASPASPWW1 - 2042 - 205
d_11ens_10METMETPHEPHEJQ1 - 1951 - 195
d_21ens_10METMETPHEPHEXX1 - 1951 - 195
d_11ens_11THRTHRGLYGLYKR1 - 2121 - 212
d_21ens_11THRTHRGLYGLYYY1 - 2121 - 212
d_11ens_12GLNGLNASPASPLS1 - 2221 - 222
d_21ens_12GLNGLNASPASPZZ1 - 2221 - 222
d_11ens_13THRTHRILEILEMT1 - 2331 - 233
d_21ens_13THRTHRILEILEaAA1 - 2331 - 233
d_11ens_14THRTHRLEULEUNU1 - 1961 - 196
d_21ens_14THRTHRLEULEUbBA1 - 1961 - 196

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6
ens_7
ens_8
ens_9
ens_10
ens_11
ens_12
ens_13
ens_14

NCS oper:
IDCodeMatrixVector
1given(-0.9989578498831, -0.0028955761466067, 0.045550299622567), (-0.0046363051124255, -0.98638593353993, -0.16438155246091), (0.045406154118477, -0.16442142729381, 0.9853445465495)65.95485365477, -290.27871845851, -26.25945036498
2given(-0.99931081437012, -0.008426416760689, 0.036150958265383), (0.0023164633346706, -0.98615188286084, -0.16582851964497), (0.037047675777967, -0.16563049064287, 0.98549176063976)65.695668516931, -290.3829087798, -25.930979240506
3given(-0.9995687735124, -0.0084723003267552, 0.02811560324947), (0.0037365050288194, -0.98638743857619, -0.16439543652201), (0.029125685383832, -0.16421949076242, 0.98599373897843)65.786965903961, -290.33773963333, -25.483940423839
4given(-0.99972588839841, -0.0033644813534614, 0.023169556129332), (-0.00061393958411677, -0.98551312535784, -0.16959806256441), (0.023404511193253, -0.16956579847551, 0.98524091918838)66.380319301633, -289.98296785626, -26.035288205442
5given(-0.99919879935616, -0.005145384309515, 0.039689852425023), (-0.0019921177550505, -0.9840777174868, -0.17772753701334), (0.039972375862122, -0.17766420845597, 0.98327902357452)65.935489782076, -289.50154045098, -27.002144642604
6given(-0.99914758665366, -0.0029409127672925, 0.04117585598697), (-0.0042151213209556, -0.98497741312366, -0.17263177108655), (0.041064983092827, -0.17265817868935, 0.98412540892676)66.076869206847, -289.79290650764, -26.645410327179
7given(-0.99910464264455, -0.0036714292990059, 0.042147759762679), (-0.0039901688746666, -0.98360962470928, -0.18026698181204), (0.042118779641174, -0.18027375512307, 0.98271429297399)65.92125620432, -289.21186497985, -27.455322700346
8given(-0.99943104605274, -0.0011646950793313, 0.033707976375008), (-0.0046584711180093, -0.98505825447438, -0.17215845590251), (0.033404832476284, -0.17221753330386, 0.98449237599382)66.716281543462, -289.73939625236, -26.247467661475
9given(-0.99939377694505, -0.0055700159119551, 0.034366459320726), (-0.00039089341533751, -0.98526128878213, -0.17105566354174), (0.034812724768975, -0.17096539927748, 0.98466182339118)66.034954631214, -290.09630460653, -26.16610220142
10given(-0.99924048655766, -0.0057945973623385, 0.038534045536725), (-0.0010653634780568, -0.98444960994223, -0.17566397036744), (0.038952728077474, -0.17557160398538, 0.98369573387777)65.893483462276, -289.9168965928, -26.947980935221
11given(-0.99938151327646, -0.0018496164190643, 0.035116518055819), (-0.0042049280880977, -0.98516512023687, -0.17155758347696), (0.034912884455975, -0.17159913982238, 0.98454803118547)66.459024772158, -289.92103476007, -26.203777230415
12given(-0.9992088909459, -0.0047327543227583, 0.039486621673408), (-0.0021498419503492, -0.98501370455355, -0.17246269167933), (0.039711087044388, -0.1724111448782, 0.98422427661968)65.970748477308, -289.85890279843, -26.297733731664
13given(-0.99936121263145, -0.0039480500786691, 0.035518721660216), (-0.0021686685039628, -0.98534776941252, -0.17054345543202), (0.035671607262912, -0.17051154275987, 0.98470977969193)66.28881539144, -289.97117915386, -26.116362086692
14given(-0.99939736566708, -0.0068079837263503, 0.034037580044334), (0.00087373901952929, -0.98520123584751, -0.17139942084111), (0.034700750392729, -0.17126638970366, 0.98461346815898)66.032844605459, -290.06435143413, -26.198895010394

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Components

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Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESGU

#1: Protein Proteasome subunit alpha type-2 / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / ...Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23639
#2: Protein Proteasome subunit alpha type-3 / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 ...Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23638
#3: Protein Proteasome subunit alpha type-4 / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component ...Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40303
#4: Protein Proteasome subunit alpha type-5 / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component ...Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32379
#5: Protein Proteasome subunit alpha type-6 / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component ...Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40302
#7: Protein Proteasome subunit alpha type-1 / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21243

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Protein , 3 types, 6 molecules FTLZMa

#6: Protein PRE10 isoform 1


Mass: 31443.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q4M4
#12: Protein PRE7 isoform 1


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0P3
#13: Protein Proteasome subunit beta


Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H8ULD3

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Proteasome endopeptidase ... , 2 types, 4 molecules HVKY

#8: Protein proteasome endopeptidase complex


Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q449, proteasome endopeptidase complex
#11: Protein proteasome endopeptidase complex


Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q5W3, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 3 types, 6 molecules IWJXNb

#9: Protein Proteasome subunit beta type-3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25451
#10: Protein Proteasome subunit beta type-4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 ...Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22141
#14: Protein Proteasome subunit beta type-1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component ...Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 3 types, 187 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.61 Å3/Da / Density % sol: 65.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: MES 100 mM pH 5.5-6.9, MPD 8-18% and magnesium acetate 20 mM
PH range: 5.5-6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 3.42→29.84 Å / Num. obs: 136674 / % possible obs: 98.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 73.208 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.106 / Rrim(I) all: 0.19 / Χ2: 1.06 / Net I/σ(I): 7.2
Reflection shellResolution: 3.42→3.48 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.8 / Num. unique obs: 6705 / CC1/2: 0.804 / Rpim(I) all: 0.573 / Rrim(I) all: 0.988 / Χ2: 1.02 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.21-5207refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.42→29.84 Å / SU ML: 0.4507 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.9391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2594 6917 5.07 %
Rwork0.2148 129416 -
obs0.2171 136333 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.7 Å2
Refinement stepCycle: LAST / Resolution: 3.42→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49061 0 22 177 49260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001849966
X-RAY DIFFRACTIONf_angle_d0.476167639
X-RAY DIFFRACTIONf_chiral_restr0.04217648
X-RAY DIFFRACTIONf_plane_restr0.00378736
X-RAY DIFFRACTIONf_dihedral_angle_d12.063218252
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.83071215632511
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.79984131009876
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.99968514770486
ens_4d_2DDX-RAY DIFFRACTIONTorsion NCS0.77835578165271
ens_5d_2EEX-RAY DIFFRACTIONTorsion NCS0.95176148367492
ens_6d_2FFX-RAY DIFFRACTIONTorsion NCS0.67652370405631
ens_7d_2GGX-RAY DIFFRACTIONTorsion NCS0.71582077421755
ens_8d_2OHX-RAY DIFFRACTIONTorsion NCS0.62708516871212
ens_9d_2PIX-RAY DIFFRACTIONTorsion NCS0.50808327350197
ens_10d_2QJX-RAY DIFFRACTIONTorsion NCS0.58555929690515
ens_11d_2RKX-RAY DIFFRACTIONTorsion NCS0.59978332567898
ens_12d_2SLX-RAY DIFFRACTIONTorsion NCS0.70282406734376
ens_13d_2TMX-RAY DIFFRACTIONTorsion NCS0.5367796021398
ens_14d_2UNX-RAY DIFFRACTIONTorsion NCS0.52348746880907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.42-3.460.44022350.35054264X-RAY DIFFRACTION97.04
3.46-3.50.40051930.33144315X-RAY DIFFRACTION97.28
3.5-3.540.37292230.32394295X-RAY DIFFRACTION98.93
3.54-3.590.42032260.30844375X-RAY DIFFRACTION98.99
3.59-3.630.32932170.2994323X-RAY DIFFRACTION99.26
3.63-3.680.37042480.29724352X-RAY DIFFRACTION99.16
3.68-3.740.34352320.28774338X-RAY DIFFRACTION99.18
3.74-3.790.34292250.28134328X-RAY DIFFRACTION98.91
3.79-3.850.31012580.27184326X-RAY DIFFRACTION98.9
3.85-3.910.31042560.25574283X-RAY DIFFRACTION98.93
3.91-3.980.32812360.25064353X-RAY DIFFRACTION99.14
3.98-4.050.30752520.24994299X-RAY DIFFRACTION98.74
4.05-4.130.31022300.22894337X-RAY DIFFRACTION98.68
4.13-4.220.25612280.21564282X-RAY DIFFRACTION97.68
4.22-4.310.25682430.21524287X-RAY DIFFRACTION98.37
4.31-4.410.27562380.2134343X-RAY DIFFRACTION98.79
4.41-4.520.24882320.20544315X-RAY DIFFRACTION98.51
4.52-4.640.25062190.20214317X-RAY DIFFRACTION98.46
4.64-4.770.24542390.19234336X-RAY DIFFRACTION98.43
4.77-4.930.23732330.19644314X-RAY DIFFRACTION98.57
4.93-5.10.23252020.1914349X-RAY DIFFRACTION98.27
5.1-5.310.27152260.20224359X-RAY DIFFRACTION98.52
5.31-5.550.26292470.2134237X-RAY DIFFRACTION97.82
5.55-5.840.27362160.21274303X-RAY DIFFRACTION98
5.84-6.20.25152070.20634312X-RAY DIFFRACTION96.95
6.2-6.670.23422370.20154329X-RAY DIFFRACTION98.81
6.67-7.330.19372150.17314363X-RAY DIFFRACTION98.45
7.34-8.380.15952530.1424290X-RAY DIFFRACTION98.02
8.38-10.480.13892110.12954255X-RAY DIFFRACTION96.29
10.48-29.840.21372400.17784237X-RAY DIFFRACTION95.24

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