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Structure of the Salmonella typhi Type I Dehydroquinase covalently inhibited by a 3-dehydroquinic 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 5.5 25% (W/V) PEG 3350, 0.1 M BIS-TRIS PH 5.5, 0.2 M MAGNESIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 2.15 42.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.399 α = 90 b = 42.327 β = 105.13 c = 84.828 γ = 90
Symmetry Space Group I 1 2 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 CCD ADSC QUANTUM 315r MIRRORS 2014-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 1.35 45.48 99.3 0.07 12.8 3.6 50525 -3 8
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 1.35 1.42 99.3 0.4 3.5 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 PDB ENTRY 1QFE 1.35 37.63 48464 2060 99.26 0.17525 0.1736 0.1831 0.21413 0.2162 RANDOM 8.938
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] 0.69 -0.66 -0.09 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.435 r_sphericity_free 22.789 r_dihedral_angle_4_deg 15.669 r_dihedral_angle_3_deg 13.173 r_dihedral_angle_1_deg 5.558 r_sphericity_bonded 5.543 r_rigid_bond_restr 1.81 r_angle_refined_deg 1.469 r_mcangle_it 1.469 r_angle_other_deg 0.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.435 r_sphericity_free 22.789 r_dihedral_angle_4_deg 15.669 r_dihedral_angle_3_deg 13.173 r_dihedral_angle_1_deg 5.558 r_sphericity_bonded 5.543 r_rigid_bond_restr 1.81 r_angle_refined_deg 1.469 r_mcangle_it 1.469 r_angle_other_deg 0.908 r_xyhbond_nbd_other 0.585 r_symmetry_hbond_other 0.517 r_symmetry_vdw_refined 0.321 r_symmetry_hbond_refined 0.275 r_nbd_refined 0.273 r_symmetry_vdw_other 0.268 r_nbd_other 0.184 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.087 r_nbtor_other 0.086 r_bond_refined_d 0.01 r_mcbond_it 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_mcbond_other 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 1919 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALE data scaling MOLREP phasing