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- PDB-5umd: Structure of the Plasmodium falciparum 80S ribosome bound to the ... -

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Entry
Database: PDB / ID: 5umd
TitleStructure of the Plasmodium falciparum 80S ribosome bound to the antimalarial drug mefloquine
Components
  • (60S ribosomal protein ...) x 39
  • (Ribosomal protein ...) x 2
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / Ribosome / protein synthesis / antimalarial
Function / homologyRibosomal protein L34Ae superfamily / Ribosomal protein L23 / Ribosomal protein L22e superfamily / Ribosomal protein L40e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e ...Ribosomal protein L34Ae superfamily / Ribosomal protein L23 / Ribosomal protein L22e superfamily / Ribosomal protein L40e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ubiquitin family / Ribosomal protein L16p/L10e / Ribosomal protein L5 / Ribosomal protein L38e superfamily / Ribosomal protein L3 / Ribosomal protein L30p/L7e / Ribosomal protein L6 / KOW motif / Ribosomal protein L13 / Ribosomal protein L4/L1 family / ribosomal L5P family C-terminus / Ribosomal L15 / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L29 protein / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L44 / Ribosomal protein L5, N-terminal / Ribosomal protein L39e domain superfamily / Ribosomal protein L15e core domain superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L4, C-terminal domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L28e/Mak16 / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L19, eukaryotic / Ribosomal protein L21 superfamily / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L32e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal L39 protein / Ribosomal L40e family / MAPK6/MAPK4 signaling / Ribosomal protein L37e signature. / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L23 signature. / Ribosomal protein L39e signature. / Ubiquitin domain signature. / Ribosomal protein L2 signature. / Ribosomal protein L3 signature. / Ribosomal protein L15 signature. / Ribosomal protein L32e signature. / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L13e signature. / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L18e signature. / Ribosomal protein L31e signature. / Ribosomal protein L34e signature. / Ribosomal protein L21e signature. / Ribosomal protein L44e signature. / Ribosomal protein L36e signature. / Ribosomal protein L15e signature. / Ribosomal protein L10e signature. / Ubiquitin domain profile. / Translesion Synthesis by POLH / L13a-mediated translational silencing of Ceruloplasmin expression / Ribosomal protein 60S L18 and 50S L18e / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L21e / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L36e / Ribosomal protein L6e / Ribosomal protein L31e / Ribosomal protein L34e / Ribosomal protein L24e / Ribosomal protein L35Ae / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L19e / Ribosomal protein L13e / Ribosomal protein L32 / Ribosomal L22e protein family / Ribosomal L18 C-terminal region / Ribosomal L27e protein family / Ribosomal L28e protein family / Ribosomal L29e protein family / Ribosomal L37ae protein family / Ribosomal L38e protein family / Ribosomal protein L37e
Function and homology information
Specimen sourcePlasmodium falciparum 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsWong, W. / Bai, X.-C. / Brown, A. / Scheres, S. / Baum, J.
CitationJournal: Nat Microbiol / Year: 2017
Title: Mefloquine targets the Plasmodium falciparum 80S ribosome to inhibit protein synthesis.
Authors: Wilson Wong / Xiao-Chen Bai / Brad E Sleebs / Tony Triglia / Alan Brown / Jennifer K Thompson / Katherine E Jackson / Eric Hanssen / Danushka S Marapana / Israel S Fernandez / Stuart A Ralph / Alan F Cowman / Sjors H W Scheres / Jake Baum
Abstract: Malaria control is heavily dependent on chemotherapeutic agents for disease prevention and drug treatment. Defining the mechanism of action for licensed drugs, for which no target is characterized, ...Malaria control is heavily dependent on chemotherapeutic agents for disease prevention and drug treatment. Defining the mechanism of action for licensed drugs, for which no target is characterized, is critical to the development of their second-generation derivatives to improve drug potency towards inhibition of their molecular targets. Mefloquine is a widely used antimalarial without a known mode of action. Here, we demonstrate that mefloquine is a protein synthesis inhibitor. We solved a 3.2 Å cryo-electron microscopy structure of the Plasmodium falciparum 80S ribosome with the (+)-mefloquine enantiomer bound to the ribosome GTPase-associated centre. Mutagenesis of mefloquine-binding residues generates parasites with increased resistance, confirming the parasite-killing mechanism. Furthermore, structure-guided derivatives with an altered piperidine group, predicted to improve binding, show enhanced parasiticidal effect. These data reveal one possible mode of action for mefloquine and demonstrate the vast potential of cryo-electron microscopy to guide the development of mefloquine derivatives to inhibit parasite protein synthesis.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 27, 2017 / Release: Mar 1, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 1, 2017Structure modelrepositoryInitial release
1.1Mar 22, 2017Structure modelDatabase references
1.2Aug 30, 2017Structure modelAuthor supporting evidence / Data collectionem_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: 28S ribosomal RNA
B: 5S ribosomal RNA
C: 5.8S ribosomal RNA
D: 60S ribosomal protein L2
E: 60S ribosomal protein L3
F: 60S ribosomal protein L4
G: 60S ribosomal protein L11a, putative
H: 60S ribosomal protein L6, putative
I: 60S ribosomal protein L6-2, putative
J: 60S ribosomal protein L7-3, putative
K: 60S ribosomal protein L13, putative
L: 60S ribosomal protein L13
M: 60S ribosomal protein L23, putative
N: 60S ribosomal protein L14, putative
O: 60S ribosomal protein L27a, putative
P: Ribosomal protein L15
Q: 60S ribosomal protein L10, putative
R: 60S ribosomal protein L5, putative
S: 60S ribosomal protein L18-2, putative
T: 60S ribosomal protein L19
U: 60S ribosomal protein L18a
V: 60S ribosomal protein L21
W: 60S ribosomal protein L17, putative
X: 60S ribosomal protein L22, putative
Y: 60S ribosomal protein L23
Z: 60S ribosomal protein L26, putative
0: 60S ribosomal protein L24, putative
1: 60S ribosomal protein L27
2: 60S ribosomal protein L28
3: 60S ribosomal protein L35, putative
4: 60S ribosomal protein L29, putative
5: 60S ribosomal protein L7, putative
6: 60S ribosomal protein L30e, putative
7: 60S ribosomal protein L31
8: 60S ribosomal protein L32
9: 60S ribosomal protein L35Ae, putative
a: 60S ribosomal protein L34
b: 60S ribosomal protein L36
c: Ribosomal protein L37
d: 60S ribosomal protein L38
e: 60S ribosomal protein L39
f: Ubiquitin-60S ribosomal protein L40
g: 60S ribosomal protein L41
h: 60S ribosomal protein L37a
i: 60S ribosomal protein L44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,136,616216
Polyers2,131,54645
Non-polymers5,070171
Water0
1


  • idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)406610
ΔGint (kcal/M)-4819
Surface area (Å2)581500
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules ABC

#1: RNA chain 28S ribosomal RNA /


Mass: 1216212.125 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank:1013064538
#2: RNA chain 5S ribosomal RNA /


Mass: 38410.859 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank:1016052399
#3: RNA chain 5.8S ribosomal RNA


Mass: 51206.461 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank:1013064403

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60S ribosomal protein ... , 39 types, 39 molecules DEFGHIJKLMNOQRSTUVWXYZ01234567...

#4: Protein/peptide 60S ribosomal protein L2 /


Mass: 28064.998 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8I3T9
#5: Protein/peptide 60S ribosomal protein L3 / / 60S ribosomal protein L3 / putative


Mass: 44318.180 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IJC6
#6: Protein/peptide 60S ribosomal protein L4 /


Mass: 46311.688 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8I431
#7: Protein/peptide 60S ribosomal protein L11a, putative /


Mass: 20268.666 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IBQ6
#8: Protein/peptide 60S ribosomal protein L6, putative /


Mass: 21638.562 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IE85
#9: Protein/peptide 60S ribosomal protein L6-2, putative /


Mass: 25587.623 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IDV1
#10: Protein/peptide 60S ribosomal protein L7-3, putative /


Mass: 32760.455 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8ILL2
#11: Protein/peptide 60S ribosomal protein L13, putative /


Mass: 23805.344 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IJZ7
#12: Protein/peptide 60S ribosomal protein L13 /


Mass: 25454.143 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IAX6
#13: Protein/peptide 60S ribosomal protein L23, putative /


Mass: 15015.713 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IE09
#14: Protein/peptide 60S ribosomal protein L14, putative /


Mass: 19340.373 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8ILE8
#15: Protein/peptide 60S ribosomal protein L27a, putative /


Mass: 16765.834 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:C6KT23
#17: Protein/peptide 60S ribosomal protein L10, putative /


Mass: 25265.480 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8ILV2
#18: Protein/peptide 60S ribosomal protein L5, putative /


Mass: 34067.352 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8ILL3
#19: Protein/peptide 60S ribosomal protein L18-2, putative /


Mass: 21508.783 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:C0H5G3
#20: Protein/peptide 60S ribosomal protein L19 /


Mass: 21641.096 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:C6KSY6
#21: Protein/peptide 60S ribosomal protein L18a /


Mass: 21793.611 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IDS6
#22: Protein/peptide 60S ribosomal protein L21 / / 60S ribosomal protein L21e / putative


Mass: 18840.244 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8ILK3
#23: Protein/peptide 60S ribosomal protein L17, putative /


Mass: 23469.926 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IDI5
#24: Protein/peptide 60S ribosomal protein L22, putative /


Mass: 16422.930 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IB51
#25: Protein/peptide 60S ribosomal protein L23 /


Mass: 22152.748 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IE82
#26: Protein/peptide 60S ribosomal protein L26, putative /


Mass: 14855.709 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:O77364
#27: Protein/peptide 60S ribosomal protein L24, putative /


Mass: 19295.930 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IEM3
#28: Protein/peptide 60S ribosomal protein L27 / / 60S ribosomal protein L27 / putative


Mass: 16785.180 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IKM5
#29: Protein/peptide 60S ribosomal protein L28 / / 60S ribosomal protein L28 / putative


Mass: 14437.823 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IHU0
#30: Protein/peptide 60S ribosomal protein L35, putative /


Mass: 14787.824 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IIB4
#31: Protein/peptide 60S ribosomal protein L29, putative / / Ribosomal protein L29 / putative


Mass: 8041.588 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:C6S3J6
#32: Protein/peptide 60S ribosomal protein L7, putative /


Mass: 30593.184 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:O97250
#33: Protein/peptide 60S ribosomal protein L30e, putative /


Mass: 11794.760 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IJK8
#34: Protein/peptide 60S ribosomal protein L31 /


Mass: 14099.854 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8I463
#35: Protein/peptide 60S ribosomal protein L32 /


Mass: 15565.751 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8I3B0
#36: Protein/peptide 60S ribosomal protein L35Ae, putative / / 60S ribosomal protein L35ae / putative


Mass: 16306.425 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IHT9
#37: Protein/peptide 60S ribosomal protein L34 /


Mass: 17406.967 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8IBY4
#38: Protein/peptide 60S ribosomal protein L36 /


Mass: 12825.440 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8I713
#40: Protein/peptide 60S ribosomal protein L38 / / 60S ribosomal protein L38e / putative


Mass: 10341.729 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8II62
#41: Protein/peptide 60S ribosomal protein L39 /


Mass: 6540.912 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:C0H4H3
#43: Protein/peptide 60S ribosomal protein L41 / / 60S ribosomal protein L41 / putative


Mass: 5108.310 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:C6S3G4
#44: Protein/peptide 60S ribosomal protein L37a /


Mass: 10826.083 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:O96184
#45: Protein/peptide 60S ribosomal protein L44 /


Mass: 12194.902 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:O97231

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Ribosomal protein ... , 2 types, 2 molecules Pc

#16: Protein/peptide Ribosomal protein L15 / Ribosome


Mass: 24197.660 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:C0H4A6
#39: Protein/peptide Ribosomal protein L37 / Ribosome


Mass: 10571.592 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:C0H4L5

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Protein/peptide , 1 types, 1 molecules f

#42: Protein/peptide Ubiquitin-60S ribosomal protein L40


Mass: 14645.169 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt:Q8ID50

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Non-polymers , 3 types, 171 molecules

#46: Chemical ChemComp-YMZ / Mefloquine


Mass: 378.312 Da / Num. of mol.: 2 / Formula: C17H16F6N2O / Mefloquine
#47: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 164 / Formula: Mg / Magnesium
#48: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Formula: Zn / Zinc

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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: Plasmodium falciparum 80S ribosome bound to mefloquine
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
Source: NATURAL
Molecular weightValue: 4.2 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Cellular location: cytoplasm / Organism: Plasmodium falciparum 3D7 (eukaryote)
Buffer solutionDetails: 20 mM Hepes pH 7.4, 40 mM KAc, 10 mM NH4Ac, 10 mM Mg(Ac)2 and 5 mM 2-mecaptoethanol
pH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Blot 2.5s before plunging / Grid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 90 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 78000 / Calibrated magnification: 104748 / Calibrated defocus min: 800 nm / Calibrated defocus max: 3800 nm / Cs: 2 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN / Temperature (max): 90 kelvins / Temperature (min): 80 kelvins
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 1
Image scansMovie frames/image: 17

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Processing

SoftwareName: REFMAC / Version: 5.8.0068 / Classification: refinement
EM software
IDNameVersionCategory
2RELION1.3image acquisition
4CTFFIND3CTF correction
7UCSF Chimeramodel fitting
9RELION1.3initial Euler assignment
10RELION1.3final Euler assignment
11RELION1.3classification
12RELION1.33D reconstruction
13REFMAC5.8model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 43184 / Symmetry type: POINT
Atomic model buildingOverall b value: 129.3 / Ref protocol: RIGID BODY FIT / Ref space: RECIPROCAL
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall SU BOverall SU MLOverall ESU RSolvent ion probe radiiSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
1129.307-0.250.090.150.17-0.020.080.9520.279210.279213.20257.50806977100.0029.1020.4280.5670.800.801.20MAXIMUM LIKELIHOOD WITH PHASESMASK
ELECTRON MICROSCOPY
Number of atoms included #1Total: 124503
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0050.014136485
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg0.8751.526196987
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg24.1856.9827685
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.18621.8972119
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.84215.00010690
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.95715.000538
ELECTRON MICROSCOPYr_chiral_restr0.3390.21322289
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02072478
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it1.34413.26824887
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it2.49619.89131002
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it1.19012.811111598
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined7.980518007
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.2 Å / R factor R work: 0.576 / Lowest resolution: 3.283 Å / Number reflection R free: 0 / Number reflection R work: 59775 / Total number of bins used: 20 / Percent reflection obs: 1

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