☰ Navigation Tabs
1.95 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) E86A Mutant in Complex with Dehydroshikimate (Crystal Form #2)
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 9 300 protein: 7.5 mg/mL in 0.5 M sodium chloride, 0.01 M Tris-HCl, crystallization condition: Qiagen PEG B6 (0.1 M MIB buffer, pH 9.0, 25% w/v PEG1500), 25 mM dehydroquinic acid crystal soak, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 1.89 34.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.838 α = 90 b = 71.671 β = 90 c = 171.755 γ = 90
Symmetry Space Group P 21 21 21
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 Beryllium lens 2012-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 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 1.95 30 99.9 0.081 3 7.1 34213 34213 -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 1.95 1.98 99.9 0.611 3 6.9 1655
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 1.95 28.63 32362 32362 1746 99.82 0.19292 0.19292 0.18994 0.1953 0.24735 0.2476 RANDOM 34.952
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] -1.11 4.4 -3.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.046 r_dihedral_angle_4_deg 14.069 r_dihedral_angle_3_deg 10.691 r_dihedral_angle_1_deg 3.152 r_angle_refined_deg 1.437 r_angle_other_deg 0.728 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.046 r_dihedral_angle_4_deg 14.069 r_dihedral_angle_3_deg 10.691 r_dihedral_angle_1_deg 3.152 r_angle_refined_deg 1.437 r_angle_other_deg 0.728 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 4002 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 23
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling