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Crystal structure of type I dehydroquinase from Salmonella typhi inhibited by a hydroxylamine derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 12% (w/v) PEG 2000 MME,
0.1 M MES-NaOH
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.503 α = 84.246 b = 43.626 β = 85.965 c = 72.372 γ = 60.935
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 2020-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 71.99 93.5 0.056 0.079 0.056 6.7 1.8 33302 15.7791
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 91.4 0.277 0.392 0.277 1.9 1.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4CNN 1.9 38.051 32893 1729 92.334 0.222 0.2183 0.2246 0.2783 0.283 34.278
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] -3.102 -0.792 1.487 2.879 -2.997 -2.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.186 r_dihedral_angle_4_deg 16.416 r_dihedral_angle_3_deg 13.683 r_dihedral_angle_1_deg 7.478 r_lrange_it 6.063 r_lrange_other 6.061 r_scangle_it 4.623 r_scangle_other 4.623 r_mcangle_other 3.687 r_mcangle_it 3.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.186 r_dihedral_angle_4_deg 16.416 r_dihedral_angle_3_deg 13.683 r_dihedral_angle_1_deg 7.478 r_lrange_it 6.063 r_lrange_other 6.061 r_scangle_it 4.623 r_scangle_other 4.623 r_mcangle_other 3.687 r_mcangle_it 3.686 r_scbond_it 3.08 r_scbond_other 3.08 r_mcbond_it 2.637 r_mcbond_other 2.635 r_angle_refined_deg 1.588 r_angle_other_deg 1.319 r_symmetry_nbd_refined 0.273 r_nbd_refined 0.214 r_nbd_other 0.186 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_refined 0.062 r_symmetry_xyhbond_nbd_other 0.057 r_chiral_restr_other 0.04 r_metal_ion_refined 0.029 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3852 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing