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1.73 Angstrom resolution crystal structure of the ABC-ATPase domain (residues 357-609) of lipid A transport protein (msbA) from Francisella tularensis subsp. tularensis SCHU S4 in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 protein: 8.2 mg/ml in 10 mM Tris-HCl pH 8.3 0.5 mM TCEP 10 mM ADP 10 mM MgCl2
crystallization: The Classics II F11 (71): 0.2 M NaCl 0.1 M Bis-Tris pH 6.5 25% (w/v) PEG 3350
cryo: crystallization condition
Crystal Properties Matthews coefficient Solvent content 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.597 α = 90 b = 70.886 β = 103.77 c = 46.647 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 MARMOSAIC 225 mm CCD 2015-08-24 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 1.73 30 90.4 0.061 20.3 5.1 23573 27.5
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 1.73 1.76 97.3 0.57 3.1 5.2
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 2fgk 1.73 21.94 22233 1199 89.78 0.19635 0.19437 0.2047 0.23282 0.2401 RANDOM 33.581
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] -3.25 -1.28 -0.11 3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.662 r_dihedral_angle_4_deg 13.583 r_dihedral_angle_3_deg 10.243 r_dihedral_angle_1_deg 3.69 r_angle_refined_deg 1.614 r_angle_other_deg 0.8 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.662 r_dihedral_angle_4_deg 13.583 r_dihedral_angle_3_deg 10.243 r_dihedral_angle_1_deg 3.69 r_angle_refined_deg 1.614 r_angle_other_deg 0.8 r_chiral_restr 0.096 r_bond_refined_d 0.011 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_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 1781 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling BALBES phasing Coot model building ARP model building