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E. coli C7 DarT1 in complex with NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OMW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294 4.0M Sodium Formate, 0.1M Sodium Acetate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.62 53.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.308 α = 90 b = 62.308 β = 90 c = 113.081 γ = 120
Symmetry Space Group P 31 2 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 XE 16M 2022-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976254 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 54.018 99.9 0.115 0.143 0.084 0.997 5.8 4.4 17764
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 2.05 99.9 1.223 1.527 0.723 0.615 0.7 4.4
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 7OMW 2 54.018 17726 792 99.73 0.198 0.1957 0.2483 0.252 42.664
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] 0.952 0.476 0.952 -3.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.959 r_dihedral_angle_3_deg 13.151 r_dihedral_angle_1_deg 6.571 r_lrange_it 6.294 r_dihedral_angle_2_deg 6.288 r_lrange_other 6.254 r_scangle_it 3.848 r_scangle_other 3.846 r_mcangle_other 3.434 r_mcangle_it 3.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.959 r_dihedral_angle_3_deg 13.151 r_dihedral_angle_1_deg 6.571 r_lrange_it 6.294 r_dihedral_angle_2_deg 6.288 r_lrange_other 6.254 r_scangle_it 3.848 r_scangle_other 3.846 r_mcangle_other 3.434 r_mcangle_it 3.433 r_scbond_it 2.392 r_scbond_other 2.391 r_mcbond_it 2.197 r_mcbond_other 2.19 r_angle_refined_deg 1.171 r_angle_other_deg 0.375 r_nbd_other 0.214 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.19 r_symmetry_nbd_refined 0.189 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.174 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.053 r_symmetry_xyhbond_nbd_other 0.025 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1704 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing