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Crystal structure of Pseudomonas aeruginosa SuhB complexed with Gallic acid in orthorhombic space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8WIP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 PEG 3350, Sodium acetate tri-hydrate
Crystal Properties Matthews coefficient Solvent content 35.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.681 α = 90 b = 90.108 β = 90 c = 90.453 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 2024-06-24 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 2.8 47.42 99.9 0.077 0.083 0.031 0.999 21.2 7.1 11742
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 2.8 2.95 100 0.433 0.466 0.171 0.913 7.3
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 2.8 35.13 11128 571 99.85 0.1818 0.17879 0.1809 0.23759 0.2273 RANDOM 54.006
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] 3.87 -3.12 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.376 r_dihedral_angle_4_deg 21.769 r_dihedral_angle_3_deg 18.802 r_long_range_B_refined 9.81 r_long_range_B_other 9.81 r_dihedral_angle_1_deg 7.318 r_scangle_other 5.051 r_mcangle_it 4.515 r_mcangle_other 4.515 r_scbond_it 3.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.376 r_dihedral_angle_4_deg 21.769 r_dihedral_angle_3_deg 18.802 r_long_range_B_refined 9.81 r_long_range_B_other 9.81 r_dihedral_angle_1_deg 7.318 r_scangle_other 5.051 r_mcangle_it 4.515 r_mcangle_other 4.515 r_scbond_it 3.056 r_scbond_other 3.042 r_mcbond_it 2.827 r_mcbond_other 2.826 r_angle_refined_deg 1.711 r_angle_other_deg 1.606 r_chiral_restr 0.108 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4066 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction PHASER phasing