2G92

Crystal Structure Analysis of the RNA Dodecamer CGC-(NF2)-AAUUAGCG, with an Incorporated 2,4-Difluorotoluyl Residue (NF2)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5291Final droplet composition: 0.5 mM oligonucleotide, 5% MPD, 20 mM sodium cacodylate, pH 5.5, 10 mM cobalt hexamine, 20 mM LiCl and 10 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9536.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.614α = 90
b = 28.614β = 90
c = 63.171γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDMARRESEARCH2004-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 5ID-B0.992APS5ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.6124.80.9780.05475387538
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.611.660.9690.53

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTModel of native A-RNA1.6124.787538742555898.550.1990.1990.1960.231RANDOM27.11
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]
1.030.521.03-1.55
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.042
r_scbond_it4.323
r_angle_refined_deg2.066
r_angle_other_deg1.504
r_xyhbond_nbd_other0.422
r_xyhbond_nbd_refined0.356
r_symmetry_hbond_refined0.311
r_nbd_other0.281
r_nbtor_refined0.251
r_nbd_refined0.182
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.042
r_scbond_it4.323
r_angle_refined_deg2.066
r_angle_other_deg1.504
r_xyhbond_nbd_other0.422
r_xyhbond_nbd_refined0.356
r_symmetry_hbond_refined0.311
r_nbd_other0.281
r_nbtor_refined0.251
r_nbd_refined0.182
r_symmetry_vdw_other0.177
r_nbtor_other0.131
r_chiral_restr0.092
r_symmetry_vdw_refined0.086
r_gen_planes_refined0.019
r_bond_refined_d0.012
r_bond_other_d0.001
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_metal_ion_refined
r_metal_ion_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 Atoms506
Solvent Atoms84
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
X-GENdata reduction
X-GENdata scaling
EPMRphasing