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- PDB-6elz: State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway o... -

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Database: PDB / ID: 6elz
TitleState E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosmes
DescriptorProteasome-interacting protein CIC1
ATP-dependent RNA helicase HAS1
Ribosome assembly factor MRT4
60S ribosome subunit biogenesis protein NIP7
Pescadillo homolog
and more 9 items
KeywordsRIBOSOME / Large Subunit Biogenesis Nucleolus
Specimen sourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
Saccharomyces cerevisiae (strain yjm789) / yeast / Baker's yeast /
MethodElectron microscopy (3.3 Å resolution / Particle / Single particle)
AuthorsKater, L. / Cheng, J. / Barrio-Garcia, C. / Hurt, E. / Beckmann, R.
CitationCell, 2017, 171, 1599-1610.e14

Cell, 2017, 171, 1599-1610.e14 Yorodumi Papers
Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.
Lukas Kater / Matthias Thoms / Clara Barrio-Garcia / Jingdong Cheng / Sherif Ismail / Yasar Luqman Ahmed / Gert Bange / Dieter Kressler / Otto Berninghausen / Irmgard Sinning / Ed Hurt / Roland Beckmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 30, 2017 / Release: Dec 27, 2017

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Structure visualization

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Assembly

Deposited unit
1: RDN25-1 25S rRNA
2: Saccharomyces cerevisiae genomic DNA sequence contains ITS1, 5.8S rRNA gene, ITS2, strain IMA 105Y
6: Saccharomyces cerevisiae culture-collection CBS:8803 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
L: 60S ribosomal protein L13-A
N: 60S ribosomal protein L15-A
Q: 60S ribosomal protein L18-A
R: 60S ribosomal protein L19-A
S: 60S ribosomal protein L20-A
T: 60S ribosomal protein L21-A
U: 60S ribosomal protein L22-A
Z: 60S ribosomal protein L27-A
c: 60S ribosomal protein L30
d: 60S ribosomal protein L31-A
e: 60S ribosomal protein L32
f: 60S ribosomal protein L33-A
g: 60S ribosomal protein L34-A
i: 60S ribosomal protein L36-A
j: 60S ribosomal protein L37-A
k: 60S ribosomal protein L38
O: 60S ribosomal protein L16-A
V: 60S ribosomal protein L23-A
a: 60S ribosomal protein L28
P: 60S ribosomal protein L17-A
X: 60S ribosomal protein L25
Y: 60S ribosomal protein L26-A
h: 60S ribosomal protein L35-A
F: 60S ribosomal protein L7-A
B: 60S ribosomal protein L3
C: 60S ribosomal protein L4-A
H: 60S ribosomal protein L9-A
A: Ribosome biogenesis protein BRX1
K: Proteasome-interacting protein CIC1
m: Ribosome biogenesis protein ERB1
D: ATP-dependent RNA helicase HAS1
W: Ribosome assembly factor MRT4
l: 60S ribosome subunit biogenesis protein NIP7
b: Nucleolar GTP-binding protein 1
o: Ribosome biogenesis protein 15
n: Pescadillo homolog
r: Ribosome biogenesis protein NSA2
s: Nuclear GTP-binding protein NUG1
t: Ribosome biogenesis protein RLP7
y: Eukaryotic translation initiation factor 6
z: UPF0642 protein YBL028C
p: Ribosome biogenesis protein YTM1
q: 25S rRNA (cytosine(2870)-C(5))-methyltransferase
u: Ribosome biogenesis protein RLP24
v: Nucleolar protein 16
w: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
I: Nucleolar complex-associated protein 3
J: rRNA-processing protein EBP2
E: 60S ribosomal protein L6-A
G: 60S ribosomal protein L8-A
M: 60S ribosomal protein L14-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,788,71555
Polyers2,788,64954
Non-polymers651
Water0
#1


  • idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)383080
ΔGint (kcal/M)-2717
Surface area (Å2)721450
MethodPISA

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Components

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Saccharomyces cerevisiae ... , 2 types, 2 molecules 26

#2: RNA chainSaccharomyces cerevisiae genomic DNA sequence contains ITS1, 5.8S rRNA gene, ITS2, strain IMA 105Y


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: 1214879358
#3: RNA chainSaccharomyces cerevisiae culture-collection CBS:8803 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence


Mass: 74308.391 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: 1102641490

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60S ribosomal protein ... , 30 types, 30 molecules LNQRSTUZcd...

#4: Polypeptide(L)60S ribosomal protein L13-A / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q12690
#5: Polypeptide(L)60S ribosomal protein L15-A / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05748
#6: Polypeptide(L)60S ribosomal protein L18-A / Large ribosomal subunit protein eL18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX49
#7: Polypeptide(L)60S ribosomal protein L19-A / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX82
#8: Polypeptide(L)60S ribosomal protein L20-A / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX23
#9: Polypeptide(L)60S ribosomal protein L21-A / Large ribosomal subunit protein eL21-A


Mass: 18279.266 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q02753
#10: Polypeptide(L)60S ribosomal protein L22-A / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05749
#11: Polypeptide(L)60S ribosomal protein L27-A / Large ribosomal subunit protein eL27-A


Mass: 15568.360 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C2H6
#12: Polypeptide(L)60S ribosomal protein L30 / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P14120
#13: Polypeptide(L)60S ribosomal protein L31-A / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12980.158 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C2H8
#14: Polypeptide(L)60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P38061
#15: Polypeptide(L)60S ribosomal protein L33-A / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05744
#16: Polypeptide(L)60S ribosomal protein L34-A / Large ribosomal subunit protein eL34-A


Mass: 13673.196 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P87262
#17: Polypeptide(L)60S ribosomal protein L36-A / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11151.259 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05745
#18: Polypeptide(L)60S ribosomal protein L37-A / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P49166
#19: Polypeptide(L)60S ribosomal protein L38 / Large ribosomal subunit protein eL38


Mass: 8845.561 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P49167
#20: Polypeptide(L)60S ribosomal protein L16-A / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P26784
#21: Polypeptide(L)60S ribosomal protein L23-A / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14493.950 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX41
#22: Polypeptide(L)60S ribosomal protein L28 / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P02406
#23: Polypeptide(L)60S ribosomal protein L17-A / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20589.518 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05740
#24: Polypeptide(L)60S ribosomal protein L25 / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P04456
#25: Polypeptide(L)60S ribosomal protein L26-A / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14265.784 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05743
#26: Polypeptide(L)60S ribosomal protein L35-A / Large ribosomal subunit protein uL29-A


Mass: 13942.640 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX84
#27: Polypeptide(L)60S ribosomal protein L7-A / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05737
#28: Polypeptide(L)60S ribosomal protein L3 / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P14126
#29: Polypeptide(L)60S ribosomal protein L4-A / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P10664
#30: Polypeptide(L)60S ribosomal protein L9-A / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05738
#52: Polypeptide(L)60S ribosomal protein L6-A / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q02326
#53: Polypeptide(L)60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P17076
#54: Polypeptide(L)60S ribosomal protein L14-A / Large ribosomal subunit protein eL14-A


Mass: 15195.066 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P36105

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Ribosome biogenesis protein ... , 7 types, 7 molecules Amortpu

#31: Polypeptide(L)Ribosome biogenesis protein BRX1


Mass: 33585.414 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q08235
#33: Polypeptide(L)Ribosome biogenesis protein ERB1 / Eukaryotic ribosome biogenesis protein 1


Mass: 91830.609 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q04660
#38: Polypeptide(L)Ribosome biogenesis protein 15 / Nucleolar protein 15


Mass: 25499.186 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P53927
#40: Polypeptide(L)Ribosome biogenesis protein NSA2 / NOP7-associated protein 2


Mass: 29786.783 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (strain YJM789) / References: UniProt: A6ZR80
#42: Polypeptide(L)Ribosome biogenesis protein RLP7 / Ribosomal protein L7-like


Mass: 36621.074 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P40693
#45: Polypeptide(L)Ribosome biogenesis protein YTM1 / Microtubule-associated protein YTM1


Mass: 51426.637 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (strain YJM789) / References: UniProt: A6ZPA9
#47: Polypeptide(L)Ribosome biogenesis protein RLP24 / Ribosomal protein L24-like


Mass: 24027.650 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q07915

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Polypeptide(L) , 11 types, 11 molecules KDWlnsyzqwJ

#32: Polypeptide(L)Proteasome-interacting protein CIC1 / Core interacting component 1


Mass: 42596.691 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P38779
#34: Polypeptide(L)ATP-dependent RNA helicase HAS1 / Helicase associated with SET1 protein 1


Mass: 56798.348 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q03532, EC: 3.6.4.13
#35: Polypeptide(L)Ribosome assembly factor MRT4 / mRNA turnover protein 4


Mass: 27098.012 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P33201
#36: Polypeptide(L)60S ribosome subunit biogenesis protein NIP7 / Nuclear import protein 7


Mass: 20411.699 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q08962
#39: Polypeptide(L)Pescadillo homolog / Nucleolar protein 7 / Ribosomal RNA-processing protein 13


Mass: 69984.148 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (strain YJM789) / References: UniProt: A6ZV85
#41: Polypeptide(L)Nuclear GTP-binding protein NUG1 / Nuclear GTPase 1


Mass: 57798.652 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P40010
#43: Polypeptide(L)Eukaryotic translation initiation factor 6 / eIF-6


Mass: 26476.605 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q12522
#44: Polypeptide(L)UPF0642 protein YBL028C


Mass: 12435.429 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P38202
#46: Polypeptide(L)25S rRNA (cytosine(2870)-C(5))-methyltransferase / Nucleolar protein 2


Mass: 69912.164 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P40991, EC: 2.1.1.310
#49: Polypeptide(L)27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase / 2'-O-ribose RNA methyltransferase SPB1 / AdoMet-dependent rRNA methyltransferase SPB1 / S-adenosyl-L-methionine-dependent methyltransferase / Suppressor of PAB1 protein 1


Mass: 96656.172 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P25582, EC: 2.1.1.167
#51: Polypeptide(L)rRNA-processing protein EBP2 / EBNA1-binding protein homolog


Mass: 49842.613 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P36049

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Nucleolar ... , 3 types, 3 molecules bvI

#37: Polypeptide(L)Nucleolar GTP-binding protein 1


Mass: 74531.227 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q02892
#48: Polypeptide(L)Nucleolar protein 16


Mass: 26954.447 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P40007
#50: Polypeptide(L)Nucleolar complex-associated protein 3


Mass: 75689.008 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q07896

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RNA chain / Non-polymers , 2 types, 2 molecules 1

#1: RNA chainRDN25-1 25S rRNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: 834774822
#55: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: TAP-Flag-Ytm1 E80A / Type: RIBOSOME
Details: Pre-60S ribosomal biogenesis intermediates purified via TAP-Flag-Ytm1 E80A
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, 54
Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 FIELD / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 27 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansSampling size: 14 microns / Dimension width: 4096 / Dimension height: 4096 / Movie frames/image: 16 / Used frames/image: 1-10

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Processing

EM software
IDNameVersionCategoryImage processing IDFitting ID
1GautomatchPARTICLE SELECTION1
4GctfCTF CORRECTION1
9REFMACMODEL REFINEMENT1
10RELIONINITIAL EULER ASSIGNMENT1
11RELION2.0FINAL EULER ASSIGNMENT1
12RELIONCLASSIFICATION1
13RELIONRECONSTRUCTION1
CTF correctionType: NONE
Particle selectionNumber of particles selected: 503000
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 112099 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Target criteria: AVERAGE FSC

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