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E. coli C7 DarT1 in complex with carba-NAD and DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 4.0 M Sodium formate, 0.1 M Tris pH 7.5
Crystal Properties Matthews coefficient Solvent content 4.02 69.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.903 α = 90 b = 61.903 β = 90 c = 215.547 γ = 90
Symmetry Space Group P 43 21 2
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 2022-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976292 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 1.92 61.9 100 0.167 0.177 0.057 0.998 8.3 9.4 33191
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 1.92 1.97 100 2.472 2.606 0.818 0.501 0.9 9.8
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 7OMZ 1.92 59.568 33112 1660 99.943 0.172 0.1704 0.1805 0.21 0.2186 34.445
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] 0.617 0.617 -1.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.434 r_dihedral_angle_3_deg 13.359 r_lrange_it 9.618 r_lrange_other 9.618 r_dihedral_angle_2_deg 7.587 r_dihedral_angle_1_deg 6.765 r_scangle_it 6.565 r_scangle_other 6.563 r_scbond_other 4.727 r_scbond_it 4.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.434 r_dihedral_angle_3_deg 13.359 r_lrange_it 9.618 r_lrange_other 9.618 r_dihedral_angle_2_deg 7.587 r_dihedral_angle_1_deg 6.765 r_scangle_it 6.565 r_scangle_other 6.563 r_scbond_other 4.727 r_scbond_it 4.726 r_mcangle_it 4.326 r_mcangle_other 4.324 r_mcbond_it 3.297 r_mcbond_other 3.297 r_angle_refined_deg 2.035 r_angle_other_deg 0.601 r_symmetry_xyhbond_nbd_refined 0.249 r_nbd_refined 0.234 r_nbd_other 0.202 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.192 r_xyhbond_nbd_refined 0.187 r_symmetry_nbd_refined 0.134 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 101 Solvent Atoms 242 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing