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Crystal structure of menaquinone-specific isochorismate synthase from Yersinia pestis CO92
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BZN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 1.6 M Ammonium sulfate
10% dioxane, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.22 44.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.19 α = 90 b = 76.997 β = 90.39 c = 70.414 γ = 90
Symmetry Space Group C 1 2 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 SBC-3 mirrors 2008-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9794 APS 19-BM
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 2.28 30 98.1 0.035 21.7 2.9 20472 20090 2 2
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 2.3 2.34 99.4 0.119 12 2.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3BZN 2.28 30 19709 19054 1029 97.12 0.19604 0.19299 0.2519 0.3004 RANDOM 17.69
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] 3.89 3.22 -1.64 -2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.771 r_dihedral_angle_3_deg 14.779 r_dihedral_angle_4_deg 14.153 r_dihedral_angle_1_deg 6.992 r_scangle_it 3.362 r_scbond_it 2.173 r_angle_refined_deg 1.477 r_mcangle_it 1.219 r_angle_other_deg 0.874 r_mcbond_it 0.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.771 r_dihedral_angle_3_deg 14.779 r_dihedral_angle_4_deg 14.153 r_dihedral_angle_1_deg 6.992 r_scangle_it 3.362 r_scbond_it 2.173 r_angle_refined_deg 1.477 r_mcangle_it 1.219 r_angle_other_deg 0.874 r_mcbond_it 0.643 r_mcbond_other 0.148 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3370 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 15
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling