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1.95 Angstrom Crystal Structure of Shikimate 5-dehydrogenase (AroE) from Salmonella enterica subsp. enterica serovar Typhimurium in Complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O9B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein solution: 7.5 mG/mL, 0.25M Sodium chloride. 0.01M Tris HCl pH 8.3, Screen solution: PEG's (H3), 0.2M Sodium phosphate, 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.16 42.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.049 α = 90 b = 111.392 β = 96.2 c = 66.38 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 CCD MARMOSAIC 225 mm CCD Beryllium lenses 2011-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.95 30 93.6 0.077 17.7 3.9 39301 39301 -3 20.8
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 1.95 1.98 97 0.501 2.8 3.9 2035
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1O9B 1.95 28.39 37240 37240 1988 93.38 0.16831 0.16831 0.16559 0.1722 0.22006 0.2244 RANDOM 25.163
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] 1.06 0.65 -0.83 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.099 r_dihedral_angle_4_deg 11.478 r_dihedral_angle_3_deg 10.441 r_scangle_it 4.745 r_scbond_it 3.058 r_dihedral_angle_1_deg 2.892 r_mcangle_it 1.762 r_angle_refined_deg 1.49 r_mcbond_it 1.032 r_angle_other_deg 0.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.099 r_dihedral_angle_4_deg 11.478 r_dihedral_angle_3_deg 10.441 r_scangle_it 4.745 r_scbond_it 3.058 r_dihedral_angle_1_deg 2.892 r_mcangle_it 1.762 r_angle_refined_deg 1.49 r_mcbond_it 1.032 r_angle_other_deg 0.844 r_mcbond_other 0.34 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4321 Nucleic Acid Atoms Solvent Atoms 582 Heterogen Atoms 98
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling