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Thermosipho africanus DarTG in complex with ADP-ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.2 M potassium thiocyanate, 0.1 M TRIS pH 7.5, 8% (w/v) PEG 20,000, 8% (v/v) PEG500MME
Crystal Properties Matthews coefficient Solvent content 2.94 58.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.458 α = 90 b = 187.458 β = 90 c = 187.458 γ = 90
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 PILATUS 6M-F 2016-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 2.96 93.73 100 0.074 0.078 0.024 1 17.3 10.7 22975
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 2.96 3.04 1.713 1.799 0.545 0.533 1.5
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 5M31 2.96 76.647 22813 1142 99.455 0.213 0.2107 0.2482 0.2258 102.859
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.398 r_dihedral_angle_3_deg 16.951 r_dihedral_angle_4_deg 16.171 r_lrange_it 7.806 r_lrange_other 7.805 r_dihedral_angle_1_deg 6.652 r_mcangle_it 4.684 r_mcangle_other 4.684 r_scangle_it 4.337 r_scangle_other 4.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.398 r_dihedral_angle_3_deg 16.951 r_dihedral_angle_4_deg 16.171 r_lrange_it 7.806 r_lrange_other 7.805 r_dihedral_angle_1_deg 6.652 r_mcangle_it 4.684 r_mcangle_other 4.684 r_scangle_it 4.337 r_scangle_other 4.337 r_mcbond_it 2.698 r_mcbond_other 2.696 r_scbond_it 2.447 r_scbond_other 2.447 r_angle_refined_deg 1.244 r_angle_other_deg 1.053 r_symmetry_xyhbond_nbd_refined 0.269 r_nbd_refined 0.179 r_nbd_other 0.179 r_symmetry_nbd_other 0.17 r_nbtor_refined 0.158 r_symmetry_nbd_refined 0.139 r_xyhbond_nbd_refined 0.099 r_symmetry_nbtor_other 0.074 r_ncsr_local_group_1 0.06 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6122 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing