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Structure of the Salmonella typhi Type I dehydroquinase 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 5.2 32% PEG 4000, 0.1 M NA-CITRATE PH 5.2
Crystal Properties Matthews coefficient Solvent content 2.1 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.67 α = 90 b = 39.406 β = 104.68 c = 155.13 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) 2013-10-08 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 1.5 150.07 88.4 0.04 14.2 2.9 131130 -3 16.7
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 1.5 1.58 50.7 0.32 2.1 1.8
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 1.5 150.07 124425 6690 88.26 0.18177 0.18005 0.1828 0.21363 0.2158 RANDOM 20.804
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] -12.53 0.42 16.29 -3.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.513 r_dihedral_angle_4_deg 17.205 r_dihedral_angle_3_deg 13.953 r_dihedral_angle_1_deg 5.827 r_scbond_it 2.487 r_mcangle_it 1.721 r_angle_refined_deg 1.276 r_mcbond_it 1.099 r_scangle_it 0.841 r_angle_other_deg 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.513 r_dihedral_angle_4_deg 17.205 r_dihedral_angle_3_deg 13.953 r_dihedral_angle_1_deg 5.827 r_scbond_it 2.487 r_mcangle_it 1.721 r_angle_refined_deg 1.276 r_mcbond_it 1.099 r_scangle_it 0.841 r_angle_other_deg 0.76 r_symmetry_vdw_refined 0.236 r_mcbond_other 0.231 r_nbd_refined 0.216 r_nbtor_refined 0.173 r_symmetry_hbond_refined 0.166 r_nbd_other 0.165 r_xyhbond_nbd_refined 0.139 r_symmetry_vdw_other 0.132 r_xyhbond_nbd_other 0.122 r_nbtor_other 0.083 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7617 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALE data scaling MOLREP phasing