3CZW | pdb_00003czw

X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JJ2a short duplex GUCU:CGGA taken from NDB: RR0033

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62931.3 M lithium sulphate, 100 mM cacodylate buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4649.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.035α = 90
b = 31.863β = 134.35
c = 39.804γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8115EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.42098.50.082196.49874987418
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.4298.90.762.55.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTa short duplex GUCU:CGGA taken from NDB: RR00331.420968696861871000.197820.1970.20.2270.22RANDOM26.537
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.572.74-1.273.54
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it2.826
r_angle_refined_deg2.483
r_scbond_it1.959
r_nbtor_refined0.284
r_nbd_refined0.18
r_xyhbond_nbd_refined0.173
r_symmetry_hbond_refined0.141
r_symmetry_vdw_refined0.124
r_chiral_restr0.104
r_bond_refined_d0.019
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it2.826
r_angle_refined_deg2.483
r_scbond_it1.959
r_nbtor_refined0.284
r_nbd_refined0.18
r_xyhbond_nbd_refined0.173
r_symmetry_hbond_refined0.141
r_symmetry_vdw_refined0.124
r_chiral_restr0.104
r_bond_refined_d0.019
r_gen_planes_refined0.016
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms303
Solvent Atoms69
Heterogen Atoms5

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling