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1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 with Nickel Bound at Active Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L2I PDB ENTRY 3L2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 Protein solution: 7.5 mg/m, 0.50 sodium phthalate, 0.01 M Tris-HCl (pH 8.3)
Screen solution: PEGs II B8 (Qiagen), 0.1 Nickel chloride, 0.1 M Tris pH 8.5, 20% (w/v) PEG 2000 MME , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.05 40.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.679 α = 90 b = 74.468 β = 100.17 c = 63.566 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 295 CCD MARMOSAIC 300 mm CCD Beryllium lens 2012-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97850 APS 21-ID-D
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 1.8 30 97.1 0.078 13.5 3.7 40064 40064 -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 1.8 1.83 86.8 0.567 1.8 2.9 1735
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 PDB ENTRY 3L2I 1.8 29.4 38018 38018 2027 96.79 0.20136 0.20136 0.19878 0.2032 0.24925 0.2507 RANDOM 39.789
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] -4.16 3.37 -1.57 4.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.231 r_dihedral_angle_4_deg 15.992 r_dihedral_angle_3_deg 11.846 r_dihedral_angle_1_deg 3.548 r_angle_refined_deg 1.763 r_angle_other_deg 0.845 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.231 r_dihedral_angle_4_deg 15.992 r_dihedral_angle_3_deg 11.846 r_dihedral_angle_1_deg 3.548 r_angle_refined_deg 1.763 r_angle_other_deg 0.845 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3806 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 14
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling