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Structural Studies of Pterin-Based Inhibitors of Dihydropteroate Synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TX0 PDB entry 1TX0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 291 LITHIUM SULFATE, propane, Bis-Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.83 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.155 α = 90 b = 99.155 β = 90 c = 262.077 γ = 120
Symmetry Space Group P 62 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 MARRESEARCH 2008-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.31 44.74 89.8 0.113 26.5 10.5 30988
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.38 56.2 0.326 4.6 6 1881
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 PDB entry 1TX0 2.31 44.74 30942 1567 89.84 0.20589 0.20283 0.2008 0.26548 0.263 RANDOM 64.685
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] 3.81 1.9 3.81 -5.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.669 r_dihedral_angle_4_deg 20.951 r_dihedral_angle_3_deg 16.975 r_dihedral_angle_1_deg 6.455 r_scangle_it 4.8 r_scbond_it 3.134 r_angle_refined_deg 1.97 r_mcangle_it 1.765 r_mcbond_it 1.135 r_symmetry_vdw_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.669 r_dihedral_angle_4_deg 20.951 r_dihedral_angle_3_deg 16.975 r_dihedral_angle_1_deg 6.455 r_scangle_it 4.8 r_scbond_it 3.134 r_angle_refined_deg 1.97 r_mcangle_it 1.765 r_mcbond_it 1.135 r_symmetry_vdw_refined 0.328 r_nbtor_refined 0.31 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.129 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4087 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 86
Software Software Software Name Purpose SERGUI data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling