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1.75 Angstrom resolution crystal structure of the apo-form acyl-carrier-protein synthase (AcpS) (acpS; purification tag off) from Staphylococcus aureus subsp. aureus COL in the I4 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JM7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 Protein (purification tag off): 4.6 mg/mL in 10 mM Tris-HCL pH 8.3, 500 mM NaCl 5 mM BME 1 mM CaCl2 150 mM imidazole
Crystallization: The PACT Suite B8(20): 200 mM Ammonium chloride 100 mM MES pH 6.0 20 % (w/v) PEG 6000
Cryo: crystallization condition
Crystal Properties Matthews coefficient Solvent content 2.27 45.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.117 α = 90 b = 103.117 β = 90 c = 71.189 γ = 90
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 2015-06-29 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) 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 1.75 30 99.9 0.077 22.86 7.4 37637 37637 24.3
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 1.75 1.78 100 0.74 2.34 6.3
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 4JM7 1.75 29.29 35751 1880 99.85 0.17027 0.16857 0.1761 0.20336 0.2089 RANDOM 29.084
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] 0.5 0.5 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.331 r_dihedral_angle_4_deg 11.971 r_dihedral_angle_3_deg 11.789 r_dihedral_angle_1_deg 4.096 r_angle_refined_deg 1.436 r_angle_other_deg 1.283 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.331 r_dihedral_angle_4_deg 11.971 r_dihedral_angle_3_deg 11.789 r_dihedral_angle_1_deg 4.096 r_angle_refined_deg 1.436 r_angle_other_deg 1.283 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.006 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 2913 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling BLU-MAX data collection PHASER phasing Coot model building HKL-2000 data reduction