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- PDB-3cw1: Crystal Structure of Human Spliceosomal U1 snRNP -

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Basic information

Entry
Database: PDB / ID: 3cw1
TitleCrystal Structure of Human Spliceosomal U1 snRNP
Components
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U1 small nuclear ribonucleoprotein ...) x 2
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • U1 snRNAU1 spliceosomal RNA
KeywordsSPLICING / pre-mRNA splicing / spliceosome / RNA-binding domain / Sm fold / zinc finger / RNA recognition motif / 5' splice site
Function / homology
Function and homology information


negative regulation of protein refolding / regulation of ATP-dependent activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation ...negative regulation of protein refolding / regulation of ATP-dependent activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / U1 snRNP binding / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / SMN-Sm protein complex / U2-type spliceosomal complex / telomerase RNA binding / telomerase holoenzyme complex / positive regulation of mRNA splicing, via spliceosome / U2-type precatalytic spliceosome / negative regulation of chaperone-mediated autophagy / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / pre-mRNA 5'-splice site binding / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA 5'-splice site recognition / U5 snRNP / Cajal body / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / single-stranded RNA binding / nuclear body / nuclear speck / mRNA binding / enzyme binding / protein homodimerization activity / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
snRNP70, RNA recognition motif / U1 small nuclear ribonucleoprotein C / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / U1-C, C2H2-type zinc finger / U1 zinc finger / Small ribonucleoprotein associated, SmB/SmN / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Small nuclear ribonucleoprotein D1 ...snRNP70, RNA recognition motif / U1 small nuclear ribonucleoprotein C / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / U1-C, C2H2-type zinc finger / U1 zinc finger / Small ribonucleoprotein associated, SmB/SmN / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Small nuclear ribonucleoprotein D1 / 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 / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / Zinc finger C2H2 superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein 70 kDa / U1 small nuclear ribonucleoprotein C / Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 ...RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein 70 kDa / U1 small nuclear ribonucleoprotein C / Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 5.493 Å
AuthorsPomeranz Krummel, D.A. / Oubridge, C. / Leung, A.K. / Li, J. / Nagai, K.
Citation
Journal: Nature / Year: 2009
Title: Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution.
Authors: Pomeranz Krummel, D.A. / Oubridge, C. / Leung, A.K. / Li, J. / Nagai, K.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs.
Authors: Kambach, C. / Walke, S. / Young, R. / Avis, J.M. / de la Fortelle, E. / Raker, V.A. / Luhrmann, R. / Li, J. / Nagai, K.
#2: Journal: Nature / Year: 2011
Title: Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis
Authors: Leung, A.K.W. / Nagai, K. / Li, J.
#3: Journal: J.Mol.Biol. / Year: 2004
Title: The structure and biochemical properties of the human spliceosomal protein U1C.
Authors: Muto, Y. / Pomeranz Krummel, D. / Oubridge, C. / Hernandez, H. / Robinson, C.V. / Neuhaus, D. / Nagai, K.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: A retroviral RNA kissing complex containing only two G.C base pairs.
Authors: Kim, C.H. / Tinoco, I.
#5: Journal: Nature / Year: 1994
Title: Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin.
Authors: Oubridge, C. / Ito, N. / Evans, P.R. / Teo, C.H. / Nagai, K.
#6: Journal: Nucleic Acids Res. / Year: 1990
Title: Solution structure of human U1 snRNA. Derivation of a possible three-dimensional model.
Authors: Krol, A. / Westhof, E. / Bach, M. / Luhrmann, R. / Ebel, J.P. / Carbon, P.
History
DepositionApr 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 31, 2011Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: U1 snRNA
v: U1 snRNA
w: U1 snRNA
x: U1 snRNA
D: Small nuclear ribonucleoprotein Sm D3
A: Small nuclear ribonucleoprotein-associated proteins B and B'
B: Small nuclear ribonucleoprotein Sm D1
C: Small nuclear ribonucleoprotein Sm D2
F: Small nuclear ribonucleoprotein F
E: Small nuclear ribonucleoprotein E
G: Small nuclear ribonucleoprotein G
K: U1 small nuclear ribonucleoprotein 70 kDa
L: U1 small nuclear ribonucleoprotein C
S: Small nuclear ribonucleoprotein Sm D3
H: Small nuclear ribonucleoprotein-associated proteins B and B'
M: Small nuclear ribonucleoprotein Sm D1
P: Small nuclear ribonucleoprotein Sm D2
Z: Small nuclear ribonucleoprotein F
W: Small nuclear ribonucleoprotein E
3: Small nuclear ribonucleoprotein G
6: U1 small nuclear ribonucleoprotein 70 kDa
9: U1 small nuclear ribonucleoprotein C
T: Small nuclear ribonucleoprotein Sm D3
I: Small nuclear ribonucleoprotein-associated proteins B and B'
N: Small nuclear ribonucleoprotein Sm D1
Q: Small nuclear ribonucleoprotein Sm D2
1: Small nuclear ribonucleoprotein F
X: Small nuclear ribonucleoprotein E
4: Small nuclear ribonucleoprotein G
7: U1 small nuclear ribonucleoprotein 70 kDa
0: U1 small nuclear ribonucleoprotein C
U: Small nuclear ribonucleoprotein Sm D3
J: Small nuclear ribonucleoprotein-associated proteins B and B'
O: Small nuclear ribonucleoprotein Sm D1
R: Small nuclear ribonucleoprotein Sm D2
2: Small nuclear ribonucleoprotein F
Y: Small nuclear ribonucleoprotein E
5: Small nuclear ribonucleoprotein G
8: U1 small nuclear ribonucleoprotein 70 kDa
l: U1 small nuclear ribonucleoprotein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)666,15744
Polymers665,89540
Non-polymers2624
Water0
1
V: U1 snRNA
D: Small nuclear ribonucleoprotein Sm D3
A: Small nuclear ribonucleoprotein-associated proteins B and B'
B: Small nuclear ribonucleoprotein Sm D1
C: Small nuclear ribonucleoprotein Sm D2
F: Small nuclear ribonucleoprotein F
E: Small nuclear ribonucleoprotein E
G: Small nuclear ribonucleoprotein G
K: U1 small nuclear ribonucleoprotein 70 kDa
L: U1 small nuclear ribonucleoprotein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,53911
Polymers166,47410
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
v: U1 snRNA
S: Small nuclear ribonucleoprotein Sm D3
H: Small nuclear ribonucleoprotein-associated proteins B and B'
M: Small nuclear ribonucleoprotein Sm D1
P: Small nuclear ribonucleoprotein Sm D2
Z: Small nuclear ribonucleoprotein F
W: Small nuclear ribonucleoprotein E
3: Small nuclear ribonucleoprotein G
6: U1 small nuclear ribonucleoprotein 70 kDa
9: U1 small nuclear ribonucleoprotein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,53911
Polymers166,47410
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
w: U1 snRNA
T: Small nuclear ribonucleoprotein Sm D3
I: Small nuclear ribonucleoprotein-associated proteins B and B'
N: Small nuclear ribonucleoprotein Sm D1
Q: Small nuclear ribonucleoprotein Sm D2
1: Small nuclear ribonucleoprotein F
X: Small nuclear ribonucleoprotein E
4: Small nuclear ribonucleoprotein G
7: U1 small nuclear ribonucleoprotein 70 kDa
0: U1 small nuclear ribonucleoprotein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,53911
Polymers166,47410
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
x: U1 snRNA
U: Small nuclear ribonucleoprotein Sm D3
J: Small nuclear ribonucleoprotein-associated proteins B and B'
O: Small nuclear ribonucleoprotein Sm D1
R: Small nuclear ribonucleoprotein Sm D2
2: Small nuclear ribonucleoprotein F
Y: Small nuclear ribonucleoprotein E
5: Small nuclear ribonucleoprotein G
8: U1 small nuclear ribonucleoprotein 70 kDa
l: U1 small nuclear ribonucleoprotein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,53911
Polymers166,47410
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.471, 127.075, 152.024
Angle α, β, γ (deg.)95.420, 105.920, 101.800
Int Tables number1
Space group name H-MP1

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Components

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Small nuclear ribonucleoprotein ... , 6 types, 24 molecules DSTUBMNOCPQRFZ12EWXYG345

#2: Protein
Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3 / Coordinate model: Cα atoms only


Mass: 13956.373 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Coexpressed with Sm B, entity 2 / Gene: SNRPD3 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009(pREP4) / References: UniProt: P62318
#4: Protein
Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1 / Coordinate model: Cα atoms only


Mass: 13310.653 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Coexpressed with Sm D2, entity 4 / Gene: SNRPD1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3, pLysS) / References: UniProt: P62314
#5: Protein
Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2 / Coordinate model: Cα atoms only


Mass: 13551.928 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Coexpressed with Sm D1, entity 3 / Gene: SNRPD2, SNRPD1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3, pLysS) / References: UniProt: P62316
#6: Protein
Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / Sm-F / SmF / Coordinate model: Cα atoms only


Mass: 9734.171 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Coexpressed with Sm E and Sm G, entities 6 and 7
Gene: SNRPF, PBSCF / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62306
#7: Protein
Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / Sm-E / SmE / Coordinate model: Cα atoms only


Mass: 10817.601 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Coexpressed with Sm F and Sm G, entities 5 and 7
Gene: SNRPE / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62304
#8: Protein
Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / Sm-G / SmG / Coordinate model: Cα atoms only


Mass: 8508.084 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Coexpressed with Sm F and Sm E, entities 5 and 6
Gene: SNRPG, PBSCG / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62308

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U1 small nuclear ribonucleoprotein ... , 2 types, 8 molecules K678L90l

#9: Protein
U1 small nuclear ribonucleoprotein 70 kDa / U1 snRNP 70 kDa / U1-70K / snRNP70 / Coordinate model: Cα atoms only


Mass: 25372.779 Da / Num. of mol.: 4 / Fragment: residues 1-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRNP70, RNPU1Z, RPU1, SNRP70, U1AP1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08621
#10: Protein
U1 small nuclear ribonucleoprotein C / U1 snRNP C / U1-C / U1C / Coordinate model: Cα atoms only


Mass: 8800.039 Da / Num. of mol.: 4 / Fragment: residues 1-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPC / Plasmid: pET3b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P09234

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RNA chain / Protein / Non-polymers , 3 types, 12 molecules VvwxAHIJ

#11: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#1: RNA chain
U1 snRNA / U1 spliceosomal RNA / Coordinate model: P atoms only


Mass: 44418.223 Da / Num. of mol.: 4
Fragment: Nucleotides 57-82 absent, replaced with kissing loop
Mutation: C53G,G54A,A55G,G56A,U83C,A85U
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: In vitro transcribed with T7 RNA polymerase / Gene: RNU1A / Plasmid: pUC
#3: Protein
Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / Sm-B/B' / SmB/B' / Coordinate model: Cα atoms only


Mass: 18003.979 Da / Num. of mol.: 4 / Fragment: residues 1-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Coexpressed with Sm D3, entity 1 / Gene: SNRPB, COD, SNRPB1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009(pREP4) / References: UniProt: P14678

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 38-40% MPD, 0.3M KCl, 0.1M MES.KOH, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2KCl11
3MES.KOH11
4MPD12
5KCl12
6MES.KOH12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11.2557,1.2511
SYNCHROTRONSLS X06SA20.9797
SYNCHROTRONSLS X06SA31.2827
SYNCHROTRONSLS X10SA40.9999
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDMar 9, 2007MIRRORS
MARMOSAIC 225 mm CCD2CCDApr 25, 2006MIRRORS
MARMOSAIC 225 mm CCD3CCDApr 25, 2006MIRRORS
MARMOSAIC 225 mm CCD4CCDSep 25, 2007MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111MADMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
3Si 111SINGLE WAVELENGTHMx-ray1
4Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.25571
21.25111
30.97971
41.28271
50.99991
ReflectionRedundancy: 7.9 % / Av σ(I) over netI: 3.8 / Number: 111105 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / D res high: 6.5 Å / D res low: 103.721 Å / Num. obs: 14148 / % possible obs: 96.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
20.55111.1187.410.0470.0477
14.5320.5595.910.0420.0427.4
11.8714.5398.510.0540.0547.8
10.2811.8798.810.0680.0687.9
9.1910.2898.910.1330.1337.9
8.399.1998.710.2830.2837.9
7.778.3998.810.4530.4537.9
7.277.7798.710.8490.8497.9
6.957.2789.311.3671.3677.9
6.956.9511.367
ReflectionResolution: 5.493→123.091 Å / Num. all: 28397 / Num. obs: 28397 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.9
Reflection shellResolution: 5.493→5.78 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.1 / Num. measured all: 31601 / Num. unique all: 4031 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.4data scaling
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
SHARPphasing
Omodel building
RefinementResolution: 5.493→123.091 Å / Num. reflection all: 28397 / Num. reflection obs: 28397 / Isotropic thermal model: Isotropic / σ(F): 0
Details: Refinement not applicable with C-alpha & phosphorous atom only model
Displacement parametersBiso mean: 231.62 Å2
Refinement stepCycle: LAST / Resolution: 5.493→123.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2809 552 4 0 3365

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