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3.0 Angstrom Crystal Structure of 3-dehydroquinate Synthase (AroB) from Francisella tularensis in Complex with NAD.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 295 Protein: 7.5 mg/ml, 0.5 M NaCl, 0.1M Tris-HCl (pH 8.3); Condition:0.2M Sodium Formate, 0.1 M Sodium Acetate (pH 5.3).
Crystal Properties Matthews coefficient Solvent content 5.5 77.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.978 α = 90 b = 178.978 β = 90 c = 96.219 γ = 120
Symmetry Space Group P 63 2 2
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 C(111) 2009-12-10 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) R Sym I (Observed) CC (Half) 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 3 30 99.8 0.067 0.067 0.887 40.4 11.6 18744 -3 94.6
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 3 3.05 100 0.814 3.3 11.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 5EKS 3 29.83 17684 968 99.71 0.15911 0.15743 0.1578 0.19223 0.1931 RANDOM 88.967
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] -1.99 -0.99 -1.99 6.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.772 r_dihedral_angle_4_deg 14.5 r_long_range_B_refined 11.729 r_dihedral_angle_3_deg 10.805 r_mcangle_it 6.437 r_scbond_it 5.602 r_mcbond_it 3.987 r_dihedral_angle_1_deg 2.196 r_angle_refined_deg 1.649 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.772 r_dihedral_angle_4_deg 14.5 r_long_range_B_refined 11.729 r_dihedral_angle_3_deg 10.805 r_mcangle_it 6.437 r_scbond_it 5.602 r_mcbond_it 3.987 r_dihedral_angle_1_deg 2.196 r_angle_refined_deg 1.649 r_chiral_restr 0.131 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2780 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing BLU-MAX data collection