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- PDB-6hrm: E. coli 70S d2d8 stapled ribosome -

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Entry
Database: PDB / ID: 6hrm
TitleE. coli 70S d2d8 stapled ribosome
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • 5S ribosomal RNA
  • stapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNA
KeywordsRIBOSOME / staple
Function / homologyRibosomal protein L13, conserved site / Ribosomal protein S6 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L36 superfamily ...Ribosomal protein L13, conserved site / Ribosomal protein S6 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L31 type A / Ribosomal protein S20 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / 30s ribosomal protein S13, C-terminal / Ribosomal protein S11 superfamily / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L19 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein S21 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein S10 domain / Ribosomal protein L28/L24 / Ribosomal protein S7p/S5e / Ribosomal protein L9, N-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L9, C-terminal / Ribosomal protein L16, conserved site / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25, short-form / Ribosomal protein L6, alpha-beta domain / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S16 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L10 / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Ribosomal protein L18e/L15P / Ribosomal protein L34, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein S12/S23 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L3, conserved site / KH domain / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S8 signature. / Ribosomal protein S7 signature. / Ribosomal protein L23 signature. / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L9, C-terminal domain / Ribosomal protein S18 signature. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal L32p protein family
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 2.96 Å resolution
AuthorsSchmied, W.H. / Tnimov, Z. / Uttamapinant, C. / Rae, C.D. / Fried, S.D. / Chin, J.W.
CitationJournal: Nature / Year: 2018
Title: Controlling orthogonal ribosome subunit interactions enables evolution of new function.
Authors: Wolfgang H Schmied / Zakir Tnimov / Chayasith Uttamapinant / Christopher D Rae / Stephen D Fried / Jason W Chin
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 27, 2018 / Release: Dec 19, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 19, 2018Structure modelrepositoryInitial release
1.1Jan 2, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
1: stapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNA
3: 5S ribosomal RNA
B: 50S ribosomal protein L2
C: 50S ribosomal protein L3
D: 50S ribosomal protein L4
E: 50S ribosomal protein L5
F: 50S ribosomal protein L6
G: 50S ribosomal protein L9
H: 50S ribosomal protein L10
I: 50S ribosomal protein L11
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
a: 50S ribosomal protein L31
b: 50S ribosomal protein L32
c: 50S ribosomal protein L33
d: 50S ribosomal protein L34
e: 50S ribosomal protein L35
f: 50S ribosomal protein L36
g: 30S ribosomal protein S2
h: 30S ribosomal protein S3
i: 30S ribosomal protein S4
j: 30S ribosomal protein S5
k: 30S ribosomal protein S6
l: 30S ribosomal protein S7
m: 30S ribosomal protein S8
n: 30S ribosomal protein S9
o: 30S ribosomal protein S10
p: 30S ribosomal protein S11
q: 30S ribosomal protein S12
r: 30S ribosomal protein S13
s: 30S ribosomal protein S14
t: 30S ribosomal protein S15
u: 30S ribosomal protein S16
v: 30S ribosomal protein S17
w: 30S ribosomal protein S18
x: 30S ribosomal protein S19
y: 30S ribosomal protein S20
z: 30S ribosomal protein S21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,159,788491
Polyers2,149,06053
Non-polymers10,728438
Water362
1


  • idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules 13

#1: RNA chain stapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNA


Mass: 1445685.000 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1370526422, GenBank: 1063812051
#2: RNA chain 5S ribosomal RNA /


Mass: 38790.090 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1403738069

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50S ribosomal protein ... , 31 types, 31 molecules BCDEFGHIJKLMNOPQRSTUVWXYZabcdef

#3: Protein/peptide 50S ribosomal protein L2 / / Large ribosomal subunit protein uL2


Mass: 29663.244 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60422
#4: Protein/peptide 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#5: Protein/peptide 50S ribosomal protein L4 / / Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60723
#6: Protein/peptide 50S ribosomal protein L5 / / Large ribosomal subunit protein uL5


Mass: 20073.234 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P62399
#7: Protein/peptide 50S ribosomal protein L6 / / Large ribosomal subunit protein uL6


Mass: 18672.418 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG55
#8: Protein/peptide 50S ribosomal protein L9 / / Large ribosomal subunit protein bL9


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R1
#9: Protein/peptide 50S ribosomal protein L10 / / 50S ribosomal protein L8 / Large ribosomal subunit protein uL10


Mass: 13981.147 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J3
#10: Protein/peptide 50S ribosomal protein L11 / / Large ribosomal subunit protein uL11


Mass: 14090.395 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J7
#11: Protein/peptide 50S ribosomal protein L13 / / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AA10
#12: Protein/peptide 50S ribosomal protein L14 / / Large ribosomal subunit protein uL14


Mass: 13565.067 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY3
#13: Protein/peptide 50S ribosomal protein L15 / / Large ribosomal subunit protein uL15


Mass: 15008.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02413
#14: Protein/peptide 50S ribosomal protein L16 / / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY7
#15: Protein/peptide 50S ribosomal protein L17 / / Large ribosomal subunit protein bL17


Mass: 13592.823 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG44
#16: Protein/peptide 50S ribosomal protein L18 / / Large ribosomal subunit protein uL18


Mass: 12663.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0C018
#17: Protein/peptide 50S ribosomal protein L19 / / Large ribosomal subunit protein bL19


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7K6
#18: Protein/peptide 50S ribosomal protein L20 / / Large ribosomal subunit protein bL20


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L3
#19: Protein/peptide 50S ribosomal protein L21 / / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG48
#20: Protein/peptide 50S ribosomal protein L22 / / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P61175
#21: Protein/peptide 50S ribosomal protein L23 / / Large ribosomal subunit protein uL23


Mass: 10661.560 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#22: Protein/peptide 50S ribosomal protein L24 / / Large ribosomal subunit protein uL24


Mass: 11208.054 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60624
#23: Protein/peptide 50S ribosomal protein L25 / / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68919
#24: Protein/peptide 50S ribosomal protein L27 / / Large ribosomal subunit protein bL27


Mass: 8275.498 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8
#25: Protein/peptide 50S ribosomal protein L28 / / Large ribosomal subunit protein bL28


Mass: 8896.354 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M2
#26: Protein/peptide 50S ribosomal protein L29 / / Large ribosomal subunit protein uL29


Mass: 7155.267 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M6
#27: Protein/peptide 50S ribosomal protein L30 / / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG51
#28: Protein/peptide 50S ribosomal protein L31 / / Large ribosomal subunit protein bL31-A


Mass: 7516.693 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M9
#29: Protein/peptide 50S ribosomal protein L32 / / Large ribosomal subunit protein bL32


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N4
#30: Protein/peptide 50S ribosomal protein L33 / / Large ribosomal subunit protein bL33


Mass: 6057.179 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N9
#31: Protein/peptide 50S ribosomal protein L34 / / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7P5
#32: Protein/peptide 50S ribosomal protein L35 / / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#33: Protein/peptide 50S ribosomal protein L36 / / Large ribosomal subunit protein bL36-A / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q6

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30S ribosomal protein ... , 20 types, 20 molecules ghijklmnopqrstuvwxyz

#34: Protein/peptide 30S ribosomal protein S2 / / Small ribosomal subunit protein uS2


Mass: 25072.867 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V0
#35: Protein/peptide 30S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 23248.994 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V3
#36: Protein/peptide 30S ribosomal protein S4 / / Small ribosomal subunit protein uS4


Mass: 23383.002 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V8
#37: Protein/peptide 30S ribosomal protein S5 / / Small ribosomal subunit protein uS5


Mass: 16475.037 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W1
#38: Protein/peptide 30S ribosomal protein S6 / / Small ribosomal subunit protein bS6


Mass: 12125.993 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#39: Protein/peptide 30S ribosomal protein S7 / / Small ribosomal subunit protein uS7


Mass: 16861.523 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359
#40: Protein/peptide 30S ribosomal protein S8 / / Small ribosomal subunit protein uS8


Mass: 14015.361 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W7
#41: Protein/peptide 30S ribosomal protein S9 / / Small ribosomal subunit protein uS9


Mass: 14554.882 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7X3
#42: Protein/peptide 30S ribosomal protein S10 / / Small ribosomal subunit protein uS10


Mass: 11254.041 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R5
#43: Protein/peptide 30S ribosomal protein S11 / / Small ribosomal subunit protein uS11


Mass: 12487.200 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9
#44: Protein/peptide 30S ribosomal protein S12 / / Small ribosomal subunit protein uS12


Mass: 13683.053 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3
#45: Protein/peptide 30S ribosomal protein S13 / / Small ribosomal subunit protein uS13


Mass: 12868.091 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S9
#46: Protein/peptide 30S ribosomal protein S14 / / Small ribosomal subunit protein uS14


Mass: 11475.364 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG59
#47: Protein/peptide 30S ribosomal protein S15 / / Small ribosomal subunit protein uS15


Mass: 10159.621 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ4
#48: Protein/peptide 30S ribosomal protein S16 / / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T3
#49: Protein/peptide 30S ribosomal protein S17 / / Small ribosomal subunit protein uS17


Mass: 9263.946 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG63
#50: Protein/peptide 30S ribosomal protein S18 / / Small ribosomal subunit protein bS18


Mass: 7734.896 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T7
#51: Protein/peptide 30S ribosomal protein S19 / / Small ribosomal subunit protein uS19


Mass: 9421.018 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U3
#52: Protein/peptide 30S ribosomal protein S20 / / Small ribosomal subunit protein bS20


Mass: 9577.268 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U7
#53: Protein/peptide 30S ribosomal protein S21 / / Small ribosomal subunit protein bS21


Mass: 8392.844 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68679

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Non-polymers , 3 types, 440 molecules

#54: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 436 / Formula: Mg / Magnesium
#55: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc
#56: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E. coli 70S d2d8 stapled ribosome / Type: RIBOSOME
Entity 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
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 27 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
4GctfCTF correction
7Coot0.8.9.2model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIX1.13-2998-000model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 94371 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingRef space: REAL
Atomic model buildingPDB-ID: 5MDZ

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