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Crystal structure of PqsD, a key enzyme in Pseudomonas aeruginosa quinolone signal biosynthesis pathway
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HN9 PDB entry 1HN9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.16 M MgCl2, 0.08M Tris-HCl pH 8.5, 24% PEG 4000, 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.94 36.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.081 α = 90 b = 90.42 β = 95.38 c = 67.894 γ = 90
Symmetry Space Group P 1 21 1
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 2008-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 27 91.4 0.091 5.1 3.1 49952
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 88.3 0.51 1.6 3.07
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 1HN9 1.8 25.6 47404 2528 91.38 0.20167 0.19822 0.2083 0.26593 0.2702 RANDOM 34.725
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] 0.51 -0.18 -0.12 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.467 r_dihedral_angle_4_deg 19.042 r_dihedral_angle_3_deg 16.97 r_sphericity_free 9.156 r_dihedral_angle_1_deg 7.401 r_sphericity_bonded 4.382 r_scangle_it 4.236 r_scbond_it 3.03 r_rigid_bond_restr 2.031 r_mcangle_it 1.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.467 r_dihedral_angle_4_deg 19.042 r_dihedral_angle_3_deg 16.97 r_sphericity_free 9.156 r_dihedral_angle_1_deg 7.401 r_sphericity_bonded 4.382 r_scangle_it 4.236 r_scbond_it 3.03 r_rigid_bond_restr 2.031 r_mcangle_it 1.926 r_angle_refined_deg 1.913 r_mcbond_it 1.312 r_symmetry_vdw_refined 0.313 r_nbtor_refined 0.306 r_xyhbond_nbd_refined 0.259 r_nbd_refined 0.241 r_symmetry_hbond_refined 0.238 r_chiral_restr 0.128 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5007 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling