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Thermus sp. 2.9 DarT in complex with ADP-ribosylated ssDNA
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 294 123 mM potassium thiocyanate, 12% (w/v) PEG2000MME
Crystal Properties Matthews coefficient Solvent content 1.87 34.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.889 α = 90 b = 38.683 β = 101.756 c = 61.012 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 1.46 38.68 100 0.132 0.144 0.057 0.995 7.4 6.4 33508
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 1.46 1.49 99.9 1.307 1.452 0.623 0.513 1.1 5.3
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE D_1292116023 1.46 32.49 33491 1622 99.958 0.164 0.1622 0.1903 0.2092 16.031
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] -0.394 -0.398 0.377 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.305 r_dihedral_angle_4_deg 22.105 r_dihedral_angle_3_deg 13.038 r_dihedral_angle_1_deg 7.026 r_lrange_it 4.484 r_lrange_other 4.353 r_scangle_it 2.397 r_scangle_other 2.396 r_angle_refined_deg 1.909 r_scbond_it 1.592
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.305 r_dihedral_angle_4_deg 22.105 r_dihedral_angle_3_deg 13.038 r_dihedral_angle_1_deg 7.026 r_lrange_it 4.484 r_lrange_other 4.353 r_scangle_it 2.397 r_scangle_other 2.396 r_angle_refined_deg 1.909 r_scbond_it 1.592 r_scbond_other 1.591 r_angle_other_deg 1.477 r_mcangle_it 1.374 r_mcangle_other 1.374 r_mcbond_it 0.913 r_mcbond_other 0.912 r_symmetry_nbd_refined 0.324 r_symmetry_xyhbond_nbd_refined 0.242 r_nbd_refined 0.241 r_nbd_other 0.241 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 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 98 Solvent Atoms 226 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing