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Thermus sp. 2.9 DarT in complex with 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 50 mM potassium thiocyanate, 20% (w/v) PEG2000MME
Crystal Properties Matthews coefficient Solvent content 2.28 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.032 α = 90 b = 61.745 β = 95.198 c = 50.197 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 EIGER2 X 16M 2019-07-08 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 1.3 35.909 97 0.041 0.045 0.017 0.999 20.3 5.9 52232
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 1.3 1.32 0.227 0.277 0.155 0.949 3.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE D_1292116023 1.3 35.909 52208 2518 96.899 0.132 0.131 0.1305 0.1525 0.1517 17.786
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] 1.524 -2.648 -0.37 -0.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.894 r_dihedral_angle_4_deg 19 r_dihedral_angle_3_deg 13.326 r_rigid_bond_restr 7.617 r_dihedral_angle_1_deg 6.76 r_lrange_it 4.176 r_scangle_it 3.827 r_lrange_other 3.817 r_scangle_other 3.811 r_scbond_it 3.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.894 r_dihedral_angle_4_deg 19 r_dihedral_angle_3_deg 13.326 r_rigid_bond_restr 7.617 r_dihedral_angle_1_deg 6.76 r_lrange_it 4.176 r_scangle_it 3.827 r_lrange_other 3.817 r_scangle_other 3.811 r_scbond_it 3.083 r_scbond_other 3.039 r_mcangle_it 2.221 r_mcangle_other 2.22 r_mcbond_it 1.817 r_mcbond_other 1.816 r_angle_refined_deg 1.803 r_angle_other_deg 1.45 r_symmetry_nbd_refined 0.353 r_nbd_refined 0.273 r_symmetry_xyhbond_nbd_refined 0.272 r_nbd_other 0.221 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.024 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1627 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing