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- PDB-1kd5: The Crystal Structure of r(GGUCACAGCCC)2 metal free form -

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Basic information

Entry
Database: PDB / ID: 1kd5
TitleThe Crystal Structure of r(GGUCACAGCCC)2 metal free form
Components5'-R(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3'
KeywordsRNA / RNA duplex
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.58 Å
AuthorsKacer, V. / Scaringe, S.A. / Scarsdale, J.N. / Rife, J.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystal structures of r(GGUCACAGCCC)2.
Authors: Kacer, V. / Scaringe, S.A. / Scarsdale, J.N. / Rife, J.P.
History
DepositionNov 12, 2001Deposition site: NDB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3'
B: 5'-R(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,9622
Polymers6,9622
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.388, 45.388, 51.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Cell settingtetragonal
Space group name H-MP43

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Components

#1: RNA chain 5'-R(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3'


Mass: 3481.146 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 50 mM tris HCl (pH 6.4), 1.4 M (NH4)2SO4, 20 mM MgCl2, 18 mM spermine, neomycin B, pH 6.4, VAPOR DIFFUSION, HANGING DROP at 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1tris HCl11
2(NH4)2SO411
3MgCl211
4spermine11
5neomycin B11
6tris HCl12
7(NH4)2SO412
8MgCl212
9spermine12
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-HCl1reservoirpH6.4
21.4 Mammonium sulfate1reservoir
320 mM1reservoirMgCl2
418 mM1reservoir
54 mg/mlprotein1drop
610 mMTris-HCl1droppH7.0
75 mM1dropMgCl2
81
91

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→25 Å / Num. all: 14792 / Num. obs: 14143 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.7
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 1.7 / Num. unique all: 721 / % possible all: 91.7
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 13635 / Redundancy: 12.1 %
Reflection shell
*PLUS
% possible obs: 91.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SHELXLrefinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.58→5 Å / Num. parameters: 5286 / Num. restraintsaints: 6608
Isotropic thermal model: Restrained Anisotropic B factors as implemented in SHELXL-96
Cross valid method: THROUGHOUT / σ(F): 2
Details: Preliminary refinement in CNS. Restrained Anisotropic B factors as implemented in SHELXL-96
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1324 9.93 %random
Rwork0.1714 ---
all0.174 ---
obs0.1714 13324 96.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-227
Refine analyzeLuzzati coordinate error obs: 0.164 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 587
Refinement stepCycle: LAST / Resolution: 1.58→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 460 0 127 587
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0.037
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
Software
*PLUS
Name: SHELXL / Version: 96 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.228 / Rfactor Rwork: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.9

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