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Crystal structure of Pseudomonas aeruginosa PqsD C112A mutant in complex with anthranilic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H77 PDB entry 3H77
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 1.96 37.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.465 α = 90 b = 59.178 β = 92.3 c = 125.993 γ = 90
Symmetry Space Group C 1 2 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 1.7 50 93.7 0.061 7.8 6.5 62039
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) 1.7 1.76 84.1 0.387 7.1 5.8
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 3H77 1.7 40 58860 3163 93.58 0.15238 0.1501 0.1494 0.19535 0.1941 RANDOM 17.183
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] 0.01 0.01 -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.214 r_dihedral_angle_4_deg 18.964 r_dihedral_angle_3_deg 12.222 r_dihedral_angle_1_deg 5.466 r_sphericity_free 3.593 r_scangle_it 2.913 r_sphericity_bonded 2.369 r_scbond_it 1.993 r_angle_refined_deg 1.337 r_mcangle_it 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.214 r_dihedral_angle_4_deg 18.964 r_dihedral_angle_3_deg 12.222 r_dihedral_angle_1_deg 5.466 r_sphericity_free 3.593 r_scangle_it 2.913 r_sphericity_bonded 2.369 r_scbond_it 1.993 r_angle_refined_deg 1.337 r_mcangle_it 1.3 r_rigid_bond_restr 1.276 r_mcbond_it 1.018 r_nbtor_refined 0.301 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.191 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5119 Nucleic Acid Atoms Solvent Atoms 655 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling