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High resolution structure of Salmonella typhi type I dehydroquinase
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 6.4 30% PEG 4000, 0.1 M CITRATE-PHOSPHATE PH 6.4
Crystal Properties Matthews coefficient Solvent content 2.1 41.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.273 α = 90 b = 44.422 β = 95.19 c = 84.711 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) 2013-11-08 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 84.36 79.3 0.03 19.7 3.6 190168 -3 8.6
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 1.05 26.5 0.43 2.3 2.6
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 51.2 186322 3823 79.04 0.13168 0.13134 0.1413 0.14872 0.1586 RANDOM 11.478
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] 0.52 0.06 -0.02 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.218 r_sphericity_free 26.658 r_dihedral_angle_4_deg 20.175 r_dihedral_angle_3_deg 13.119 r_sphericity_bonded 6.155 r_scbond_it 6.013 r_dihedral_angle_1_deg 5.509 r_mcangle_it 4.433 r_mcbond_it 3.225 r_scangle_it 2.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.218 r_sphericity_free 26.658 r_dihedral_angle_4_deg 20.175 r_dihedral_angle_3_deg 13.119 r_sphericity_bonded 6.155 r_scbond_it 6.013 r_dihedral_angle_1_deg 5.509 r_mcangle_it 4.433 r_mcbond_it 3.225 r_scangle_it 2.463 r_mcbond_other 1.378 r_angle_refined_deg 1.264 r_rigid_bond_restr 1.144 r_angle_other_deg 0.778 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.249 r_symmetry_vdw_other 0.202 r_nbtor_refined 0.174 r_nbd_other 0.169 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.132 r_nbtor_other 0.084 r_chiral_restr 0.077 r_xyhbond_nbd_other 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3782 Nucleic Acid Atoms Solvent Atoms 752 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALE data scaling MOLREP phasing