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Thermus sp. 2.9 DarT in complex with carba-NAD+ and 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 50 mM potassium thiocyanate, 10% (w/v) PEG2000MME
Crystal Properties Matthews coefficient Solvent content 1.95 36.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.499 α = 90 b = 39.104 β = 99.461 c = 61.636 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 PILATUS 6M-F 2019-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 1.6 39.11 99.9 0.092 0.104 0.047 0.996 7.4 4.3 26615
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 1.6 1.64 0.803 0.939 0.479 0.625 1.3
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 1.6 37.542 26597 1345 99.827 0.164 0.1622 0.1968 0.2007 21.741
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] -0.819 -0.653 -0.222 1.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.802 r_dihedral_angle_4_deg 19.903 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_1_deg 7.265 r_lrange_it 4.291 r_lrange_other 4.222 r_scangle_it 2.699 r_scangle_other 2.697 r_angle_refined_deg 1.845 r_scbond_it 1.759
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.802 r_dihedral_angle_4_deg 19.903 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_1_deg 7.265 r_lrange_it 4.291 r_lrange_other 4.222 r_scangle_it 2.699 r_scangle_other 2.697 r_angle_refined_deg 1.845 r_scbond_it 1.759 r_scbond_other 1.756 r_mcangle_other 1.652 r_mcangle_it 1.651 r_angle_other_deg 1.454 r_mcbond_it 1.11 r_mcbond_other 1.106 r_symmetry_xyhbond_nbd_refined 0.204 r_nbd_other 0.203 r_nbd_refined 0.197 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.185 r_symmetry_nbd_refined 0.139 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.013 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 99 Solvent Atoms 151 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing