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Structure of Salmonella typhi type I dehydroquinase irreversibly inhibited with a 1,3,4-trihydroxyciclohexane-1-carboxylic 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 5.6 34% PEG 4000, 0.1 M CITRATE-PHOSPHATE PH 5.6
Crystal Properties Matthews coefficient Solvent content 2.1 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.59 α = 90 b = 44.47 β = 95.17 c = 84.98 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) 2013-03-08 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 1.4 47.17 96 0.06 12.8 3.6 85495 -3 9.2
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 1.4 1.48 76.1 0.22 4.1 2.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QFE 1.4 47.21 81186 4293 95.95 0.12168 0.1199 0.1343 0.15498 0.1639 RANDOM 12.231
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] 0.16 -0.47 0.69 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.369 r_sphericity_free 28.717 r_dihedral_angle_4_deg 15.135 r_dihedral_angle_3_deg 13.353 r_scbond_it 8.568 r_sphericity_bonded 7.921 r_mcangle_it 7.551 r_mcbond_it 5.7767 r_dihedral_angle_1_deg 5.678 r_scangle_it 4.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.369 r_sphericity_free 28.717 r_dihedral_angle_4_deg 15.135 r_dihedral_angle_3_deg 13.353 r_scbond_it 8.568 r_sphericity_bonded 7.921 r_mcangle_it 7.551 r_mcbond_it 5.7767 r_dihedral_angle_1_deg 5.678 r_scangle_it 4.247 r_mcbond_other 2.2897 r_rigid_bond_restr 1.847 r_angle_refined_deg 1.533 r_angle_other_deg 0.947 r_symmetry_vdw_refined 0.287 r_nbd_refined 0.284 r_symmetry_hbond_refined 0.2645 r_symmetry_vdw_other 0.243 r_nbtor_refined 0.172 r_nbd_other 0.171 r_xyhbond_nbd_refined 0.163 r_metal_ion_refined 0.151 r_xyhbond_nbd_other 0.119 r_chiral_restr 0.091 r_nbtor_other 0.083 r_symmetry_hbond_other 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_metal_ion_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 3790 Nucleic Acid Atoms Solvent Atoms 665 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALE data scaling MOLREP phasing