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Crystallographic Structure of a Dodecameric RNA-DNA Hybrid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZBI PDB ENTRY 1ZBI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 20% PEG 3350, 0.2 M magnesium formate, 10% 2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.79 55.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.649 α = 90 b = 44.459 β = 105.27 c = 83.346 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU SATURN 92 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 26.27 99.9 0.086 13.4 7.3 8314 47.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 99.9 0.492 2.7 7.3
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 PDB ENTRY 1ZBI 2.8 26.27 7484 796 99.53 0.23874 0.23837 0.2395 0.24204 0.2551 RANDOM 29.455
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] 0.85 0.04 1.83 -2.35
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 2.221 r_angle_refined_deg 1.698 r_chiral_restr 0.084 r_gen_planes_refined 0.016 r_gen_planes_other 0.014 r_bond_other_d 0.012 r_bond_refined_d 0.009 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 2.221 r_angle_refined_deg 1.698 r_chiral_restr 0.084 r_gen_planes_refined 0.016 r_gen_planes_other 0.014 r_bond_other_d 0.012 r_bond_refined_d 0.009 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_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other 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 1980 Solvent Atoms 1 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Coot model building CrystalClear data collection d*TREK data scaling PHASER phasing