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Crystal Structure of the Multidrug effulx transporter BpeF from Burkholderia pseudomallei.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.7 298 50mM N-(2-Acetamido)iminodiacetic acid, 100mM Lithium Chloride, 200mM Ammonium Sulfate, 36% PEG 300
Crystal Properties Matthews coefficient Solvent content 3 59.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.875 α = 97.39 b = 121.141 β = 111.19 c = 159.745 γ = 100.6
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 EIGER X 16M 2020-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3 49.02 99.47 0.094 0.997 8.5 5.3 160880
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 93.07 0.661 0.608 0.9 1.84
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4DX5 3 49.02 1.95 160486 7874 99.61 0.2133 0.211 0.2111 0.2588 0.2591
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.693 f_angle_d 1.263 f_chiral_restr 0.069 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 47539 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 245
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHENIX phasing Coot model building MolProbity model building