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Crystal structure of Pseudomonas aeruginosa PqsD in a covalent complex with anthranilate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H76 PDB entry 3H76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2 M MgCl2, 0.1M Tris-HCl pH 8.5, 21% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.894 α = 90 b = 59.656 β = 103.95 c = 83.427 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 CCD ADSC QUANTUM 315 2009-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 NSLS X29A
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 50 99.7 0.068 7.8 7 59980
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 99.3 0.402 6.2 6.1
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 3H76 1.8 30 56914 3026 99.63 0.15409 0.15186 0.1532 0.19488 0.1951 RANDOM 25.632
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] -0.06 0.06 0.16 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.851 r_dihedral_angle_4_deg 17.561 r_dihedral_angle_3_deg 13.973 r_dihedral_angle_1_deg 6.796 r_sphericity_free 4.501 r_scangle_it 3.401 r_scbond_it 3.074 r_rigid_bond_restr 2.897 r_sphericity_bonded 2.82 r_angle_refined_deg 1.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.851 r_dihedral_angle_4_deg 17.561 r_dihedral_angle_3_deg 13.973 r_dihedral_angle_1_deg 6.796 r_sphericity_free 4.501 r_scangle_it 3.401 r_scbond_it 3.074 r_rigid_bond_restr 2.897 r_sphericity_bonded 2.82 r_angle_refined_deg 1.663 r_mcangle_it 1.46 r_mcbond_it 1.15 r_nbtor_refined 0.305 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.213 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.142 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5160 Nucleic Acid Atoms Solvent Atoms 582 Heterogen Atoms 114
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling