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Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with Succinic Acid
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 292 Protein: 7.0 mg/ml, 0.5M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM Succinic acid;
Screen: Classics II (H9), 0.05M Zing acetate, 20% (w/v) PEG 3350;
Cryo: Reservoir.
Crystal Properties Matthews coefficient Solvent content 1.97 37.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.585 α = 78.78 b = 44.495 β = 84.22 c = 47.239 γ = 75.83
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 300 mm CCD 2022-04-08 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) R Sym I (Observed) Rrim I (All) 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 1.35 30 95.4 0.103 0.103 0.121 0.063 0.987 13.4 3.7 55717 -3 13.7
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 1.35 1.37 92.9 0.894 0.559 2 4
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 SAD THROUGHOUT 1.35 29.85 52942 2775 95.22 0.17365 0.17282 0.1744 0.18922 0.1919 RANDOM 20.752
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] 0.15 0.02 -0.73 0.12 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 8.356 r_long_range_B_refined 5.595 r_long_range_B_other 5.52 r_dihedral_angle_1_deg 4.31 r_scangle_other 3.484 r_dihedral_angle_2_deg 2.436 r_scbond_it 2.224 r_scbond_other 2.224 r_mcangle_it 1.58 r_mcangle_other 1.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 8.356 r_long_range_B_refined 5.595 r_long_range_B_other 5.52 r_dihedral_angle_1_deg 4.31 r_scangle_other 3.484 r_dihedral_angle_2_deg 2.436 r_scbond_it 2.224 r_scbond_other 2.224 r_mcangle_it 1.58 r_mcangle_other 1.579 r_angle_refined_deg 1.461 r_mcbond_it 1.022 r_mcbond_other 1.021 r_angle_other_deg 0.497 r_chiral_restr 0.082 r_gen_planes_refined 0.019 r_gen_planes_other 0.016 r_bond_refined_d 0.005 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2411 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing