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Crystal structure of the staphylococcal efflux pump QacA in the outward open state bound to ethidium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1M carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1M buffer system 1 (Imidazole; MES monohydrate) pH 6.5 and 50% precipitant mix 3 (40% v/v Glycerol; 20% w/v PEG 4000)
Crystal Properties Matthews coefficient Solvent content 3.56 65.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.281 α = 90 b = 169.861 β = 90 c = 61.779 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER2 XE 16M 2021-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 2.789 110.843 91.1 0.022 0.998 14.4 26.3 14427 101.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.789 3.214 0.453 0.808
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.79 110.84 13681 746 36.72 0.32312 0.32148 0.3152 0.35111 0.3382 RANDOM 41.163
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] -0.33 0.39 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.555 r_dihedral_angle_3_deg 16.52 r_dihedral_angle_1_deg 2.968 r_angle_refined_deg 1.555 r_angle_other_deg 0.5 r_chiral_restr 0.089 r_long_range_B_refined 0.079 r_long_range_B_other 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.555 r_dihedral_angle_3_deg 16.52 r_dihedral_angle_1_deg 2.968 r_angle_refined_deg 1.555 r_angle_other_deg 0.5 r_chiral_restr 0.089 r_long_range_B_refined 0.079 r_long_range_B_other 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d r_dihedral_angle_4_deg 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7295 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing