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- PDB-5d99: 3DW4 redetermined by direct methods starting from random phase angles -

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Basic information

Entry
Database: PDB / ID: 5d99
Title3DW4 redetermined by direct methods starting from random phase angles
ComponentsRNA (27-MER) hairpin from sarcin-ricin domain of E. coli 23S rRNA
KeywordsRNA / ab initio direct methods structure determination / hairpin RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEnterobacteria phage L1 (virus)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 0.97 Å
AuthorsMooers, B.H.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI088011 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20 GM103640 United States
CitationJournal: RNA / Year: 2009
Title: A fast selenium derivatization strategy for crystallization and phasing of RNA structures.
Authors: Olieric, V. / Rieder, U. / Lang, K. / Serganov, A. / Schulze-Briese, C. / Micura, R. / Dumas, P. / Ennifar, E.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references / Experimental preparation ...Database references / Experimental preparation / Other / Structure summary
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0This entry 5D99 reflects an alternative modeling of the structural data in r3dw4SF original data ...This entry 5D99 reflects an alternative modeling of the structural data in r3dw4SF original data determined by Author: V.Olieric,U.Rieder,K.Lang,A.Serganov,C.Schulze-Briese,R.Micura,P.Dumas,E.Ennifar

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (27-MER) hairpin from sarcin-ricin domain of E. coli 23S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8502
Polymers8,7581
Non-polymers921
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.630, 29.630, 76.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: RNA chain RNA (27-MER) hairpin from sarcin-ricin domain of E. coli 23S rRNA


Mass: 8758.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage L1 (virus)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.7 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3DW4.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassification
PHENIX1.10_2142refinement
Sir2014phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.97→20.952 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 10.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1199 2029 5.23 %Random selection
Rwork0.1046 ---
obs0.1054 38814 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.97→20.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 580 6 172 758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006758
X-RAY DIFFRACTIONf_angle_d1.2241184
X-RAY DIFFRACTIONf_dihedral_angle_d15.737376
X-RAY DIFFRACTIONf_chiral_restr0.05153
X-RAY DIFFRACTIONf_plane_restr0.0231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.99430.19121410.18082644X-RAY DIFFRACTION99
0.9943-1.02120.16351380.15192650X-RAY DIFFRACTION100
1.0212-1.05120.13021510.12732603X-RAY DIFFRACTION100
1.0512-1.08520.1251360.11292614X-RAY DIFFRACTION100
1.0852-1.12390.1161520.1062609X-RAY DIFFRACTION100
1.1239-1.16890.11881310.12618X-RAY DIFFRACTION100
1.1689-1.22210.10921580.09492597X-RAY DIFFRACTION100
1.2221-1.28660.10661360.09142671X-RAY DIFFRACTION100
1.2866-1.36720.11181630.09812595X-RAY DIFFRACTION100
1.3672-1.47270.1281310.10382640X-RAY DIFFRACTION100
1.4727-1.62080.11231460.09882628X-RAY DIFFRACTION100
1.6208-1.85530.10991470.09562629X-RAY DIFFRACTION100
1.8553-2.33690.1231500.11322622X-RAY DIFFRACTION100
2.3369-20.95650.12151490.10192665X-RAY DIFFRACTION100

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