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X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JJ2 a short duplex GUCU:CGGA taken from NDB: RR0033
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 1.3 M lithium sulphate, 100 mM cacodylate buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.035 α = 90 b = 31.863 β = 134.35 c = 39.804 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2004-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8115 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.4 20 98.5 0.082 19 6.4 9874 9874 18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.42 98.9 0.76 2.5 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT a short duplex GUCU:CGGA taken from NDB: RR0033 1.4 20 9686 9686 187 100 0.19782 0.197 0.1961 0.227 0.2186 RANDOM 26.537
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] 1.57 2.74 -1.27 3.54
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.826 r_angle_refined_deg 2.483 r_scbond_it 1.959 r_nbtor_refined 0.284 r_nbd_refined 0.18 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.141 r_symmetry_vdw_refined 0.124 r_chiral_restr 0.104 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.826 r_angle_refined_deg 2.483 r_scbond_it 1.959 r_nbtor_refined 0.284 r_nbd_refined 0.18 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.141 r_symmetry_vdw_refined 0.124 r_chiral_restr 0.104 r_bond_refined_d 0.019 r_gen_planes_refined 0.016 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 Atoms Number Protein Atoms Nucleic Acid Atoms 303 Solvent Atoms 69 Heterogen Atoms 5
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling