5MWI

Crystal structure of G(CUG)8G duplex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5292magnesium acetate, cacodylate and lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.1943.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.514α = 90
b = 43.514β = 90
c = 198.101γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252014-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.515099.90.0450.9921.87.41184625
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.511.699.80.82.17.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4E481.5137.021124959399.890.194880.191710.25621RANDOM28.937
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]
-1.3-0.65-1.34.2
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.954
r_sphericity_bonded21.028
r_long_range_B_other6.016
r_long_range_B_refined5.982
r_scangle_other5.951
r_rigid_bond_restr5.539
r_scbond_it5.078
r_scbond_other5.067
r_angle_refined_deg2.128
r_angle_other_deg1.903
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.954
r_sphericity_bonded21.028
r_long_range_B_other6.016
r_long_range_B_refined5.982
r_scangle_other5.951
r_rigid_bond_restr5.539
r_scbond_it5.078
r_scbond_other5.067
r_angle_refined_deg2.128
r_angle_other_deg1.903
r_chiral_restr0.099
r_gen_planes_refined0.025
r_bond_refined_d0.017
r_gen_planes_other0.016
r_bond_other_d0.003
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms544
Solvent Atoms71
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing