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E. coli C7 DarT1 in complex with ADP-ribosylated ssDNA and nicotinamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 4.0 M Sodium formate, 0.1 M Tris pH 7.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.759 α = 90 b = 61.759 β = 90 c = 215.039 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2022-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976277 Diamond I03
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 1.63 61.74 100 0.072 0.076 0.025 0.999 14 9 53204
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 1.63 1.66 100 1.581 1.677 0.551 0.701 1.3 9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7OMZ 1.63 46.832 53097 2675 99.891 0.156 0.155 0.1664 0.1779 0.1869 24.661
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] 0.706 0.706 -1.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.748 r_dihedral_angle_3_deg 13.339 r_lrange_it 7.292 r_lrange_other 6.874 r_dihedral_angle_2_deg 6.676 r_dihedral_angle_1_deg 6.197 r_scangle_it 4.469 r_scangle_other 4.468 r_scbond_it 3.09 r_scbond_other 3.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.748 r_dihedral_angle_3_deg 13.339 r_lrange_it 7.292 r_lrange_other 6.874 r_dihedral_angle_2_deg 6.676 r_dihedral_angle_1_deg 6.197 r_scangle_it 4.469 r_scangle_other 4.468 r_scbond_it 3.09 r_scbond_other 3.089 r_mcangle_it 2.424 r_mcangle_other 2.423 r_angle_refined_deg 1.889 r_mcbond_other 1.824 r_mcbond_it 1.823 r_angle_other_deg 0.624 r_symmetry_xyhbond_nbd_refined 0.313 r_nbd_other 0.248 r_nbd_refined 0.223 r_symmetry_nbd_refined 0.221 r_nbtor_refined 0.191 r_symmetry_nbd_other 0.185 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1704 Nucleic Acid Atoms 101 Solvent Atoms 356 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing