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Crystal structure of Pseudomonas aeruginosa SuhB complexed with Magnesium sulfate and myo-Inositol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8WIP Pseudomonas aeruginosa SuhB apo form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 Sodium acetate trihydrate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.645 α = 90 b = 89.43 β = 90 c = 102.969 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 IMAGE PLATE MAR scanner 345 mm plate 2024-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97893 RRCAT INDUS-2 PX-BL21
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 2.4 48.27 100 0.093 0.102 0.043 0.998 15.4 5.7 20413
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 2.4 2.53 100 0.578 0.636 0.263 0.856 3.3 5.7
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 2.4 48.27 19287 1078 99.96 0.1809 0.17804 0.1829 0.232 0.226 RANDOM 41.996
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] 2.76 -2.13 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.485 r_dihedral_angle_2_deg 7.712 r_long_range_B_refined 7.55 r_long_range_B_other 7.414 r_dihedral_angle_1_deg 6.746 r_scangle_other 5.244 r_mcangle_it 4.321 r_mcangle_other 4.32 r_scbond_it 3.197 r_scbond_other 3.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.485 r_dihedral_angle_2_deg 7.712 r_long_range_B_refined 7.55 r_long_range_B_other 7.414 r_dihedral_angle_1_deg 6.746 r_scangle_other 5.244 r_mcangle_it 4.321 r_mcangle_other 4.32 r_scbond_it 3.197 r_scbond_other 3.171 r_mcbond_it 2.646 r_mcbond_other 2.645 r_angle_refined_deg 1.624 r_angle_other_deg 0.56 r_chiral_restr 0.078 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 4019 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing