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Crystal Structure of the Staphylococcus aureus Enoyl-Acyl Carrier Protein Reductase (FabI) in apo form (one molecule in AU)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PD3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 10~15% PEG 400, 0.1M Tris pH 8.3~8.5, 4% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.58 52.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.877 α = 90 b = 74.716 β = 90 c = 110.652 γ = 90
Symmetry Space Group I 2 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 ADSC QUANTUM 270 2008-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6C1 1.000 PAL/PLS 6C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.7 50 98 0.08 0.28 19 8 7634 7261 2 2 43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 56 0.13 0.28 2.95 3.4 451
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PD3 2.706 37.66 7261 7261 347 91.81 0.21476 0.21099 0.2186 0.28857 0.2903 RANDOM 42.514
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] -0.3 -0.5 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.95 r_dihedral_angle_4_deg 31.784 r_dihedral_angle_3_deg 26.358 r_dihedral_angle_1_deg 14.036 r_scangle_it 7.319 r_scbond_it 4.598 r_angle_refined_deg 3.86 r_mcangle_it 3.239 r_mcbond_it 1.765 r_symmetry_hbond_refined 0.979
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.95 r_dihedral_angle_4_deg 31.784 r_dihedral_angle_3_deg 26.358 r_dihedral_angle_1_deg 14.036 r_scangle_it 7.319 r_scbond_it 4.598 r_angle_refined_deg 3.86 r_mcangle_it 3.239 r_mcbond_it 1.765 r_symmetry_hbond_refined 0.979 r_symmetry_vdw_refined 0.447 r_nbtor_refined 0.37 r_nbd_refined 0.366 r_chiral_restr 0.309 r_xyhbond_nbd_refined 0.282 r_metal_ion_refined 0.189 r_bond_refined_d 0.048 r_gen_planes_refined 0.013 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 1704 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling