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Crystal structure of type I dehydroquinase from Salmonella typhi inhibited by an epoxide 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 7 291 26 % (w/v) PEG 2000 MME,
0.1 M HEPES-NaOH
Crystal Properties Matthews coefficient Solvent content 1.9 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.713 α = 90 b = 47.08 β = 90 c = 105.2 γ = 90
Symmetry Space Group P 2 21 21
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 2015-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.00556 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.55 105.2 89.4 0.036 0.041 0.019 1 22.6 4.1 28123 13.361
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.63 73.4 0.398 0.452 0.209 0.903 3.4 3.8
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 (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 1.55 52.6 27996 1366 88.595 0.168 0.1668 0.1796 0.1997 0.212 16.196
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] -0.236 -0.358 0.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.77 r_dihedral_angle_4_deg 20.107 r_dihedral_angle_3_deg 13.299 r_dihedral_angle_1_deg 6.647 r_lrange_it 4.484 r_lrange_other 4.455 r_scangle_it 3.604 r_scangle_other 3.554 r_scbond_it 2.421 r_scbond_other 2.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.77 r_dihedral_angle_4_deg 20.107 r_dihedral_angle_3_deg 13.299 r_dihedral_angle_1_deg 6.647 r_lrange_it 4.484 r_lrange_other 4.455 r_scangle_it 3.604 r_scangle_other 3.554 r_scbond_it 2.421 r_scbond_other 2.338 r_mcangle_other 2.13 r_mcangle_it 2.119 r_angle_refined_deg 1.758 r_angle_other_deg 1.52 r_mcbond_it 1.426 r_mcbond_other 1.358 r_nbd_refined 0.221 r_symmetry_nbd_refined 0.218 r_nbd_other 0.211 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.154 r_xyhbond_nbd_refined 0.146 r_xyhbond_nbd_other 0.094 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.082 r_chiral_restr_other 0.024 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1936 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing