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Structure of the Salmonella typhi type I dehydroquinase inhibited by a 3-epiquinic acid derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QFE PDB ENTRY 1QFE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.4 30% PEG 4000, 0.1 M CITRATE-PHOSPHATE PH 6.4
Crystal Properties Matthews coefficient Solvent content 2.1 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.216 α = 90 b = 44.473 β = 95.2 c = 84.702 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M PLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR) 2013-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC ALBA XALOC
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 1.15 84.35 98.6 0.05 12.9 3.1 156242 -3 8.3
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 1.15 1.21 95.9 0.33 3.2 2.6
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 PDB ENTRY 1QFE 1.15 51.17 153096 3124 98.51 0.13396 0.13344 0.1449 0.16031 0.1709 RANDOM 11.232
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] 0.21 -0.25 -0.03 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.237 r_sphericity_free 22.142 r_dihedral_angle_4_deg 14.715 r_dihedral_angle_3_deg 12.905 r_scbond_it 6.021 r_sphericity_bonded 5.697 r_dihedral_angle_1_deg 5.695 r_mcangle_it 5.096 r_mcbond_it 3.724 r_scangle_it 2.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.237 r_sphericity_free 22.142 r_dihedral_angle_4_deg 14.715 r_dihedral_angle_3_deg 12.905 r_scbond_it 6.021 r_sphericity_bonded 5.697 r_dihedral_angle_1_deg 5.695 r_mcangle_it 5.096 r_mcbond_it 3.724 r_scangle_it 2.797 r_mcbond_other 1.494 r_rigid_bond_restr 1.358 r_angle_refined_deg 1.354 r_angle_other_deg 0.784 r_nbd_refined 0.244 r_symmetry_vdw_refined 0.237 r_symmetry_vdw_other 0.206 r_nbtor_refined 0.175 r_nbd_other 0.171 r_xyhbond_nbd_refined 0.138 r_metal_ion_refined 0.095 r_nbtor_other 0.085 r_symmetry_hbond_refined 0.085 r_chiral_restr 0.076 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_xyhbond_nbd_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3860 Nucleic Acid Atoms Solvent Atoms 668 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALE data scaling MOLREP phasing