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1.95 Angstrom Crystal Structure of of Type I 3-Dehydroquinate Dehydratase (aroD) from Clostridium difficile with Covalent Modified Comenic Acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JS3 PDB ENTRY 3JS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Protein: 7.5mg/mL, 0.5M Sodium cloride, 0.01M Tris-HCl pH 8.3.
Screen: 0.1M MES pH 6.5, 25% (v/v) PEG 550 MME. VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.37 48.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.275 α = 90 b = 138.688 β = 90.01 c = 66.315 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 Beryllium lenses 2009-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 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 99.8 0.067 17.4 3.8 79221 79221 -3 24.7
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 99.6 0.458 3.1 3.8 3903
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 3JS3 1.95 27.64 74846 74846 4014 99.75 0.15788 0.15788 0.15561 0.1639 0.19936 0.205 RANDOM 24.372
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] 1.09 -0.21 0.5 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.274 r_dihedral_angle_4_deg 12.156 r_dihedral_angle_3_deg 10.365 r_scangle_it 5.469 r_scbond_it 3.474 r_dihedral_angle_1_deg 3.469 r_mcangle_it 2.091 r_angle_other_deg 1.974 r_angle_refined_deg 1.325 r_mcbond_it 1.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.274 r_dihedral_angle_4_deg 12.156 r_dihedral_angle_3_deg 10.365 r_scangle_it 5.469 r_scbond_it 3.474 r_dihedral_angle_1_deg 3.469 r_mcangle_it 2.091 r_angle_other_deg 1.974 r_angle_refined_deg 1.325 r_mcbond_it 1.238 r_mcbond_other 0.42 r_chiral_restr 0.085 r_bond_refined_d 0.013 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 8036 Nucleic Acid Atoms Solvent Atoms 817 Heterogen Atoms 94
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling