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- PDB-5gam: Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP -

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Entry
Database: PDB / ID: 5gam
TitleFoot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Components
  • (Pre-mRNA-splicing factor ...) x 2
  • (Small nuclear ribonucleoprotein ...) x 6
  • Small nuclear ribonucleoprotein-associated protein B
  • U5 snRNA
  • U6 snRNA, 5' end
  • Unknown polypeptide
KeywordsTRANSCRIPTION / pre-mRNA splicing / snRNP / GTPase / U5 snRNA / Prp8 / spliceosome
Function / homology
Function and homology information


generation of catalytic spliceosome for first transesterification step / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / snRNP binding / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex ...generation of catalytic spliceosome for first transesterification step / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / snRNP binding / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / poly(U) RNA binding / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / Prp19 complex / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / GTPase activity / mRNA binding / GTP binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / SH3 type barrels. - #100 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G ...: / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / SH3 type barrels. - #100 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / Elongation factor Tu domain 2 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / SH3 type barrels. / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribonuclease H-like superfamily / Roll / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing factor SNU114 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 ...GUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing factor SNU114 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.7 Å
AuthorsNguyen, T.H.D. / Galej, W.P. / Bai, X.C. / Oubridge, C. / Scheres, S.H.W. / Newman, A.J. / Nagai, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
Citation
Journal: Nature / Year: 2016
Title: Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution.
Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-Chen Bai / Chris Oubridge / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai /
Abstract: U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led ...U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.
#1: Journal: Nature / Year: 2015
Title: The architecture of the spliceosomal U4/U6.U5 tri-snRNP.
Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-chen Bai / Christos G Savva / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai /
Abstract: U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key ...U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key components Prp8, Brr2 and Snu114. The tri-snRNP combines with a precursor messenger RNA substrate bound to U1 and U2 small nuclear ribonucleoprotein particles (snRNPs), and transforms into a catalytically active spliceosome after extensive compositional and conformational changes triggered by unwinding of the U4 and U6 (U4/U6) snRNAs. Here we use cryo-electron microscopy single-particle reconstruction of Saccharomyces cerevisiae tri-snRNP at 5.9 Å resolution to reveal the essentially complete organization of its RNA and protein components. The single-stranded region of U4 snRNA between its 3' stem-loop and the U4/U6 snRNA stem I is loaded into the Brr2 helicase active site ready for unwinding. Snu114 and the amino-terminal domain of Prp8 position U5 snRNA to insert its loop I, which aligns the exons for splicing, into the Prp8 active site cavity. The structure provides crucial insights into the activation process and the active site of the spliceosome.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: em_imaging_optics / em_software ...em_imaging_optics / em_software / pdbx_audit_support / struct_conn / struct_conn_type
Item: _em_imaging_optics.energyfilter_name / _em_software.name ..._em_imaging_optics.energyfilter_name / _em_software.name / _em_software.version / _pdbx_audit_support.funding_organization
Revision 1.2Oct 2, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
U: U5 snRNA
A: Pre-mRNA-splicing factor 8
C: Pre-mRNA-splicing factor SNU114
W: U6 snRNA, 5' end
b: Small nuclear ribonucleoprotein-associated protein B
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
x: Unknown polypeptide
d: Small nuclear ribonucleoprotein Sm D3
h: Small nuclear ribonucleoprotein Sm D1
j: Small nuclear ribonucleoprotein Sm D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,48513
Polymers359,96212
Non-polymers5231
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35960 Å2
ΔGint-246 kcal/mol
Surface area107930 Å2
MethodPISA

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Components

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RNA chain , 2 types, 2 molecules UW

#1: RNA chain U5 snRNA


Mass: 57138.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Short form of U5 snRNA (179 nt) / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: GenBank: 807071959
#4: RNA chain U6 snRNA, 5' end


Mass: 9928.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The 5' end 31 nucleotides of U6 snRNA / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123

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Pre-mRNA-splicing factor ... , 2 types, 2 molecules AC

#2: Protein Pre-mRNA-splicing factor 8 / Prp8 / N-terminal domain


Mass: 85826.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P33334
#3: Protein Pre-mRNA-splicing factor SNU114 / 114 kDa U5 small nuclear ribonucleoprotein component / Growth inhibitory protein 10 / Snu114


Mass: 114132.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Full length Snu114 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P36048

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Small nuclear ribonucleoprotein ... , 6 types, 6 molecules efgdhj

#6: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE / U5 SmE


Mass: 10385.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The SmE protein from the U5 snRNP Sm protein ring. / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: Q12330
#7: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9669.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The SmF protein from the U5 snRNP Sm protein ring. / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P54999
#8: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8490.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The SmG protein from the U5 snRNP Sm protein ring. / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P40204
#10: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3 / U5 SmD3


Mass: 11240.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The SmD3 protein from the U5 snRNP Sm protein ring.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P43321
#11: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / snRNP core protein D1 / U5 SmD1


Mass: 16296.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The SmD1 protein from the U5 snRNP Sm protein ring.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: Q02260
#12: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2 / SmD2


Mass: 12876.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The SmD2 protein from the U5 snRNP Sm protein ring.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: Q06217

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Protein / Protein/peptide / Non-polymers , 3 types, 3 molecules bx

#13: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Protein Small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / SmB / U5 SmB


Mass: 22426.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The SmB protein from the U5 snRNP Sm protein ring. / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P40018
#9: Protein/peptide Unknown polypeptide


Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Molecular weightValue: 0.35 MDa
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123
Buffer solutionpH: 7.9
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHepes.KOH1
2150 mMpotassium chlorideKCl1
31 mMmagnesium acetateMg(CH3COO)21
41 mMDTT1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportDetails: Grids are made of holey carbon, carbon-coated and glow discharged in N-amylamine.
Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 35714 X / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm / Cs: 2 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 16 sec. / Electron dose: 38 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2477
EM imaging opticsEnergyfilter name: GIF Quantum
Image scansMovie frames/image: 20 / Used frames/image: 1-20

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Processing

SoftwareName: REFMAC / Version: 5.8.0124 / Classification: refinement
EM software
IDNameVersionCategory
1RELIONparticle selection
2DigitalMicrographimage acquisition
4CTFFIND4CTF correction
7Coot0.8.3model fitting
9REFMAC5.8model refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 473827
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140155 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSpace: RECIPROCAL
RefinementResolution: 3.7→154.44 Å / Cor.coef. Fo:Fc: 0.971 / SU B: 29.01 / SU ML: 0.411 / ESU R: 0.682
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.287 --
obs0.287 122835 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 382.847 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å26.37 Å20.49 Å2
2--2.07 Å21.88 Å2
3----3.8 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.01819995
ELECTRON MICROSCOPYr_bond_other_d0.0020.0217081
ELECTRON MICROSCOPYr_angle_refined_deg1.3881.82227772
ELECTRON MICROSCOPYr_angle_other_deg1.047339291
ELECTRON MICROSCOPYr_dihedral_angle_1_deg12.8375.3852080
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.96223.459610
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.525152647
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.9221588
ELECTRON MICROSCOPYr_chiral_restr0.220.2053260
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.02119672
ELECTRON MICROSCOPYr_gen_planes_other0.0020.024456
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_it20.72437.8588057
ELECTRON MICROSCOPYr_mcbond_other20.72537.8568056
ELECTRON MICROSCOPYr_mcangle_it31.17556.7510038
ELECTRON MICROSCOPYr_mcangle_other31.17456.75210039
ELECTRON MICROSCOPYr_scbond_it20.39840.95411938
ELECTRON MICROSCOPYr_scbond_other20.39740.95511939
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other32.51260.95217735
ELECTRON MICROSCOPYr_long_range_B_refined41.90540349
ELECTRON MICROSCOPYr_long_range_B_other41.90540349
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.7→3.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork3.61 9041 -
Rfree-0 -
obs--100 %

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