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Crystal structure of a DNA-RNA chimera in complex with Ba2+ ions: a case of unusual multi-domain twinning
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P4J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 292 A 1.5 MM WATER SOLUTION OF DNA-RNA MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE*4HCL, 80 MM NACL, 20 MM BACL2, 40 MM SODIUM CACODYLATE AND EQUILIBRATED AGAINST 35% MPD, PH 6.0
Crystal Properties Matthews coefficient Solvent content 1.65 25.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.72 α = 90 b = 44.1 β = 119.98 c = 35.72 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 RAYONIX MX-225 2012-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.8266 BESSY 14.2
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 1.09 30.94 99.4 0.071 13.07 5.84 40052 40052 11.719
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 1.09 1.12 99.5 0.375 3.12 3.33
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 FREE R-VALUE 3P4J 1.09 30.94 40051 101 99.74 0.11361 0.115 0.1168 0.169 0.1494 Using the 'thin resolution shells' method 11.814
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] -0.5 -13.14 -0.49 0.99
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 27.212 r_sphericity_bonded 15.429 r_rigid_bond_restr 12.445 r_long_range_B_refined 5.164 r_long_range_B_other 4.391 r_scangle_other 4.367 r_scbond_other 3.649 r_scbond_it 3.648 r_angle_refined_deg 1.888 r_angle_other_deg 1.698
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 27.212 r_sphericity_bonded 15.429 r_rigid_bond_restr 12.445 r_long_range_B_refined 5.164 r_long_range_B_other 4.391 r_scangle_other 4.367 r_scbond_other 3.649 r_scbond_it 3.648 r_angle_refined_deg 1.888 r_angle_other_deg 1.698 r_chiral_restr 0.14 r_bond_refined_d 0.018 r_gen_planes_refined 0.015 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 984 Solvent Atoms 224 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing