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Crystal Structure of S. pneumoniae Enoyl-Acyl Carrier Protein Reductase (FabK) in Complex with an Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 8-15% PEG 1000, 8-15% MPD, 0.1M MES pH 5.5-7.0, 0.1M ammonium chloride, 0.2M calcium chloride, 5mM dithiothreitol
, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.25 45.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.63 α = 90 b = 126.485 β = 112.04 c = 53.522 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 RIGAKU JUPITER 210 A fixed exit Si double crystal monochromator followed byStandard double crystal monochromator and Rh-coated downward-deflection mirror with a typical glancing angle of 3.7 mrad. 2005-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.0000 SPring-8 BL32B2
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 2.3 29.08 91.9 0.083 9.2 3 25448 27.024
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) 2.3 2.38 90 0.163 4.5 2.9
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 THROUGHOUT 2Z6I 2.3 29.08 24154 1288 91.86 0.25226 0.24946 0.2501 0.30638 0.3048 RANDOM 23.443
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] -0.52 -2.62 -2.73 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.865 r_dihedral_angle_3_deg 16.873 r_dihedral_angle_4_deg 15.084 r_dihedral_angle_1_deg 5.486 r_scangle_it 1.74 r_angle_refined_deg 1.216 r_scbond_it 1.092 r_mcangle_it 0.756 r_mcbond_it 0.433 r_symmetry_hbond_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.865 r_dihedral_angle_3_deg 16.873 r_dihedral_angle_4_deg 15.084 r_dihedral_angle_1_deg 5.486 r_scangle_it 1.74 r_angle_refined_deg 1.216 r_scbond_it 1.092 r_mcangle_it 0.756 r_mcbond_it 0.433 r_symmetry_hbond_refined 0.32 r_nbtor_refined 0.294 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.188 r_xyhbond_nbd_refined 0.142 r_metal_ion_refined 0.132 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4507 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement BSS data collection CrystalClear data reduction CrystalClear data scaling