☰ Navigation Tabs
2.4 Angstrom resolution crystal structure of shikimate 5-dehydrogenase (aroE) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with shikimate and NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PGJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Protein: 6.8 mg/mL in 10 mM Tris/HCl pH 8.3, 0.25 M NaCl, 5 mM BME. Soak: 5 mM NADPH, 5 mM dehydroshikimate. Crystallization: PEGsII (B11: 0.2 M Na acetate, 0.1 M HEPES pH 7.5, 20 % (w/v) PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2 38.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.03 α = 90 b = 86.079 β = 92.85 c = 81.018 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 300 mm CCD Be-Lenses 2010-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G
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 2.4 30 99.9 0.055 18.92 3.8 41040 41040 -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) 1 2.4 2.44 100 0.57 2.31 3.8
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 3PGJ 2.4 29.48 38956 38956 2059 99.7 0.23666 0.23459 0.2363 0.2756 0.2805 RANDOM 57.938
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] -0.19 1.04 1.64 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 9.844 r_dihedral_angle_3_deg 2.834 r_scangle_it 2.49 r_dihedral_angle_4_deg 1.965 r_scbond_it 1.481 r_angle_refined_deg 1.267 r_mcangle_it 1.087 r_angle_other_deg 0.797 r_mcbond_it 0.573 r_dihedral_angle_1_deg 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 9.844 r_dihedral_angle_3_deg 2.834 r_scangle_it 2.49 r_dihedral_angle_4_deg 1.965 r_scbond_it 1.481 r_angle_refined_deg 1.267 r_mcangle_it 1.087 r_angle_other_deg 0.797 r_mcbond_it 0.573 r_dihedral_angle_1_deg 0.45 r_chiral_restr 0.117 r_mcbond_other 0.084 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8076 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 120
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling