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Crystal structure of G(CUG)8G duplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 magnesium acetate, cacodylate and lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.19 43.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.514 α = 90 b = 43.514 β = 90 c = 198.101 γ = 120
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 RAYONIX MX-225 2014-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.51 50 99.9 0.045 0.99 21.8 7.4 11846 25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.6 99.8 0.8 2.1 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4E48 1.51 37.02 11249 593 99.89 0.19488 0.19171 0.2015 0.25621 0.2715 RANDOM 28.937
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 -1.3 4.2
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.954 r_sphericity_bonded 21.028 r_long_range_B_other 6.016 r_long_range_B_refined 5.982 r_scangle_other 5.951 r_rigid_bond_restr 5.539 r_scbond_it 5.078 r_scbond_other 5.067 r_angle_refined_deg 2.128 r_angle_other_deg 1.903
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.954 r_sphericity_bonded 21.028 r_long_range_B_other 6.016 r_long_range_B_refined 5.982 r_scangle_other 5.951 r_rigid_bond_restr 5.539 r_scbond_it 5.078 r_scbond_other 5.067 r_angle_refined_deg 2.128 r_angle_other_deg 1.903 r_chiral_restr 0.099 r_gen_planes_refined 0.025 r_bond_refined_d 0.017 r_gen_planes_other 0.016 r_bond_other_d 0.003 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 Atoms Number Protein Atoms Nucleic Acid Atoms 544 Solvent Atoms 71 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing