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Crystal Structure of FolP (dihydropteroate synthase) from Colstridium difficile in the presence of pteroic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 2.4-2.6 M ammonium sulfate, 200 mM LiCl, 100 mM CHES (pH 9), 4 mM pteroic acid
Crystal Properties Matthews coefficient Solvent content 5.01 75.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.258 α = 90 b = 156.258 β = 90 c = 84.708 γ = 120
Symmetry Space Group P 63 2 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 CCD ADSC QUANTUM 210r 2018-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.99861 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 50 99.2 0.098 45.4 13 41365
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 99.5 0.454 4.3 7.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4hb7 2 37.56 39244 2116 98.93 0.1895 0.1876 0.2238 0.2138 RANDOM 39.817
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] -1.63 -0.81 -1.63 5.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.698 r_dihedral_angle_3_deg 15.964 r_dihedral_angle_4_deg 15.207 r_dihedral_angle_1_deg 6.493 r_angle_refined_deg 1.753 r_angle_other_deg 0.549 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.698 r_dihedral_angle_3_deg 15.964 r_dihedral_angle_4_deg 15.207 r_dihedral_angle_1_deg 6.493 r_angle_refined_deg 1.753 r_angle_other_deg 0.549 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2061 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing