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Catalytic domain of E.coli dihydrolipoamide succinyltransferase in I4 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C4T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 50 mM Tris pH 8.0
2.6 M NaCl
Crystal Properties Matthews coefficient Solvent content 3.33 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.598 α = 90 b = 128.598 β = 90 c = 249.733 γ = 90
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 EIGER X 9M 2018-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3 47.36 82.9 0.22 0.125 0.98 3.7 3.7 33570 60.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 85.5 1.47 0.86 0.34 0.8 3.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1C4T 3 47.36 31857 1641 82.83 0.2324 0.23031 0.229 0.27172 0.2695 RANDOM 76.611
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] 0.07 0.07 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.376 r_dihedral_angle_4_deg 16.243 r_dihedral_angle_3_deg 15.417 r_long_range_B_refined 12.444 r_long_range_B_other 12.443 r_mcangle_it 9.055 r_mcangle_other 9.055 r_scangle_other 7.925 r_dihedral_angle_1_deg 5.951 r_mcbond_it 5.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.376 r_dihedral_angle_4_deg 16.243 r_dihedral_angle_3_deg 15.417 r_long_range_B_refined 12.444 r_long_range_B_other 12.443 r_mcangle_it 9.055 r_mcangle_other 9.055 r_scangle_other 7.925 r_dihedral_angle_1_deg 5.951 r_mcbond_it 5.711 r_mcbond_other 5.711 r_scbond_it 4.823 r_scbond_other 4.823 r_angle_refined_deg 1.539 r_angle_other_deg 1.043 r_chiral_restr 0.051 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10962 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling SIMBAD phasing