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DNA-imidazolium-bridged dinucleotide intermediate complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.05 M HEPES pH 7.0, 0.2 M Ammonium acetate, 0.15 M Magnesium acetate, 10% w/v Polyethylene glycol 6,000.
Crystal Properties Matthews coefficient Solvent content 3.13 60.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.241 α = 90 b = 48.241 β = 90 c = 82.663 γ = 120
Symmetry Space Group P 3 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 99 PIXEL DECTRIS EIGER X 16M 2022-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033175 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.557 50 92.4 0.052 0.057 0.023 0.988 49.6 6.5 15265
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.557 1.59 55.2 0.438 0.498 0.231 0.965 2.6 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.557 41.778 15265 768 92.291 0.206 0.2039 0.2074 0.2494 0.2368 48.136
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] -0.007 -0.003 -0.007 0.022
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 8.029 r_lrange_other 7.577 r_scangle_it 6.98 r_scangle_other 6.978 r_scbond_it 5.119 r_scbond_other 5.116 r_angle_other_deg 3.476 r_angle_refined_deg 2.933 r_chiral_restr_other 1.552 r_nbtor_refined 0.253
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 8.029 r_lrange_other 7.577 r_scangle_it 6.98 r_scangle_other 6.978 r_scbond_it 5.119 r_scbond_other 5.116 r_angle_other_deg 3.476 r_angle_refined_deg 2.933 r_chiral_restr_other 1.552 r_nbtor_refined 0.253 r_symmetry_nbtor_other 0.237 r_symmetry_nbd_other 0.201 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.176 r_nbd_other 0.175 r_symmetry_xyhbond_nbd_refined 0.162 r_symmetry_nbd_refined 0.16 r_metal_ion_refined 0.114 r_nbd_refined 0.09 r_dihedral_angle_other_2_deg 0.051 r_bond_other_d 0.026 r_bond_refined_d 0.02 r_gen_planes_refined 0.015 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 598 Solvent Atoms 130 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing