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Crystal structure of PA0884, the SBP component of a Pseudomonas aeruginosa PAO1 Tripartite ATP-independent Periplasmic (TRAP) transporter, complexed with itaconate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q9I561-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 JCSG-plus HT-96 D12: 0.04 M Potassium phosphate monobasic, 16 % w/v PEG 8000, 20 % v/v Glycerol
Crystal Properties Matthews coefficient Solvent content 2.39 48.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.206 α = 90 b = 117.49 β = 90 c = 166.063 γ = 90
Symmetry Space Group P 21 21 21
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 2023-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 50.07 100 0.308 0.333 0.126 0.995 7.1 13.1 63463
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 3.617 3.908 1.469 0.354 13.6
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 1.8 50.07 60163 3204 99.98 0.18783 0.18541 0.1961 0.23205 0.2256 RANDOM 25.042
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] -2.25 0.62 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.768 r_dihedral_angle_2_deg 13.172 r_long_range_B_refined 7.792 r_dihedral_angle_1_deg 6.634 r_scbond_it 5.148 r_mcangle_it 3.386 r_mcbond_it 2.656 r_angle_refined_deg 2.575 r_chiral_restr 0.164 r_bond_refined_d 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.768 r_dihedral_angle_2_deg 13.172 r_long_range_B_refined 7.792 r_dihedral_angle_1_deg 6.634 r_scbond_it 5.148 r_mcangle_it 3.386 r_mcbond_it 2.656 r_angle_refined_deg 2.575 r_chiral_restr 0.164 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 4885 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing