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2.49 Angstrom resolution crystal structure of shikimate 5-dehydrogenase (aroE) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with shikimate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 295 Protein: 7.5 mg/mL in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystallization condition: The Classic suite H3 (#87) condition (0.2 M Ammonium acetate, 0.1 M tri-Sodium citrate pH 5.6, 30 % (w/v) PEG4000). Crystal was soaked in 25 mM shikimate. , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.9 35.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.527 α = 90 b = 83.657 β = 93.51 c = 79.585 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 Be-Lenses/Diamond Laue Mono 2010-10-20 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 2.5 30 100 0.058 20.77 3.8 34293 34293 -3
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) 2.5 2.54 100 0.525 2.41 3.8 1679
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 (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 3O8Q 2.49 28.8 32555 32555 1723 98.68 0.19609 0.19338 0.2036 0.24711 0.254 RANDOM 59.66
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] -1.5 0.58 0.42 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.359 r_dihedral_angle_3_deg 5.85 r_dihedral_angle_4_deg 4.198 r_scangle_it 3.103 r_scbond_it 1.848 r_angle_refined_deg 1.416 r_mcangle_it 1.132 r_dihedral_angle_1_deg 0.938 r_angle_other_deg 0.825 r_mcbond_it 0.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.359 r_dihedral_angle_3_deg 5.85 r_dihedral_angle_4_deg 4.198 r_scangle_it 3.103 r_scbond_it 1.848 r_angle_refined_deg 1.416 r_mcangle_it 1.132 r_dihedral_angle_1_deg 0.938 r_angle_other_deg 0.825 r_mcbond_it 0.578 r_mcbond_other 0.107 r_chiral_restr 0.083 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8261 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 48
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling