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E. coli Dihydropteroate Synthase in complex with pterin-based inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 50 mM Tris, 32-50% Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.53 51.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.721 α = 90 b = 94.551 β = 90 c = 136.846 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 CCD MARMOSAIC 225 mm CCD 2021-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 2.14 68.42 98.2 0.12 0.131 0.051 0.998 18.1 11.8 31532 25.27
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 2.14 2.2 91.3 0.626 0.771 0.443 0.722 2.4 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.141 68.42 31477 1490 97.983 0.194 0.1921 0.1921 0.238 0.2379 RANDOM 28.506
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] -0.849 -0.511 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.954 r_dihedral_angle_3_deg 12.617 r_lrange_it 6.668 r_dihedral_angle_1_deg 6.124 r_dihedral_angle_2_deg 5.337 r_scangle_it 5.234 r_mcangle_it 3.642 r_scbond_it 3.619 r_mcbond_it 2.46 r_angle_refined_deg 1.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.954 r_dihedral_angle_3_deg 12.617 r_lrange_it 6.668 r_dihedral_angle_1_deg 6.124 r_dihedral_angle_2_deg 5.337 r_scangle_it 5.234 r_mcangle_it 3.642 r_scbond_it 3.619 r_mcbond_it 2.46 r_angle_refined_deg 1.626 r_nbtor_refined 0.304 r_nbd_refined 0.212 r_symmetry_nbd_refined 0.172 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.129 r_chiral_restr 0.104 r_ncsr_local_group_1 0.096 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3885 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement Aimless data scaling Coot model building REFMAC phasing XDS data reduction