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Thermus sp. 2.9 DarT in complex with carba-NAD+
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 64 mM potassium thiocyanate, 20% (w/v) PEG2000MME
Crystal Properties Matthews coefficient Solvent content 2.19 43.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.034 α = 90 b = 71.282 β = 90 c = 85.542 γ = 90
Symmetry Space Group P 21 21 21
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 X 16M 2019-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.52 54.77 99.3 0.1 0.109 0.043 0.997 8.8 6 33587
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 1.52 1.56 0.932 1.072 0.514 0.581 1.2
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 D_1292116023 1.52 42.771 33520 1642 99.139 0.175 0.1733 0.185 0.2027 0.214 18.143
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] -1.115 1.053 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.206 r_dihedral_angle_4_deg 15.148 r_dihedral_angle_3_deg 12.444 r_dihedral_angle_1_deg 6.775 r_lrange_it 4.43 r_lrange_other 4.242 r_scangle_it 2.195 r_scangle_other 2.171 r_angle_refined_deg 1.53 r_scbond_it 1.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.206 r_dihedral_angle_4_deg 15.148 r_dihedral_angle_3_deg 12.444 r_dihedral_angle_1_deg 6.775 r_lrange_it 4.43 r_lrange_other 4.242 r_scangle_it 2.195 r_scangle_other 2.171 r_angle_refined_deg 1.53 r_scbond_it 1.433 r_mcangle_it 1.418 r_mcangle_other 1.418 r_scbond_other 1.379 r_angle_other_deg 1.356 r_mcbond_it 0.874 r_mcbond_other 0.872 r_symmetry_xyhbond_nbd_refined 0.218 r_nbd_other 0.215 r_symmetry_nbd_refined 0.214 r_nbd_refined 0.195 r_nbtor_refined 0.181 r_symmetry_nbd_other 0.177 r_xyhbond_nbd_other 0.166 r_xyhbond_nbd_refined 0.14 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1607 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing