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Thermus sp. 2.9 DarT in complex with ADP-ribosylated ssDNA and nicotinamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OMV D_1292116023
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 150 mM potassium thiocyanate, 10% (w/v) PEG2000MME
Crystal Properties Matthews coefficient Solvent content 1.88 34.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.963 α = 90 b = 38.89 β = 101.805 c = 61.179 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 PIXEL DECTRIS PILATUS3 6M 2019-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.8998 Diamond I24
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 1.66 38.89 98.1 0.134 0.149 0.063 0.992 6.6 5.3 22671
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 1.66 1.69 80.7 0.622 0.721 0.356 0.722 1.6 3.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE D_1292116023 1.66 37.685 22657 1076 98.023 0.153 0.1512 0.1805 0.1955 17.738
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] -1.027 0.269 0.866 0.045
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.347 r_dihedral_angle_4_deg 23.795 r_dihedral_angle_3_deg 12.32 r_dihedral_angle_1_deg 7.275 r_lrange_it 4.859 r_lrange_other 4.638 r_scangle_it 2.732 r_scangle_other 2.731 r_angle_refined_deg 1.847 r_scbond_it 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.347 r_dihedral_angle_4_deg 23.795 r_dihedral_angle_3_deg 12.32 r_dihedral_angle_1_deg 7.275 r_lrange_it 4.859 r_lrange_other 4.638 r_scangle_it 2.732 r_scangle_other 2.731 r_angle_refined_deg 1.847 r_scbond_it 1.71 r_scbond_other 1.71 r_mcangle_it 1.585 r_mcangle_other 1.585 r_angle_other_deg 1.405 r_mcbond_it 1.055 r_mcbond_other 1.051 r_nbd_refined 0.236 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.168 r_nbd_other 0.167 r_symmetry_xyhbond_nbd_refined 0.161 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.083 r_symmetry_nbd_refined 0.066 r_gen_planes_refined 0.014 r_bond_refined_d 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1724 Nucleic Acid Atoms 99 Solvent Atoms 202 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing