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Structure of Pseudomonas Quinolone Signal Response Protein PqsE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 292 100mM HEPES, 200mM MgCl2, 30% PEG 400, 5mM bis-pNPP, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.28 46.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.98 α = 90 b = 60.98 β = 90 c = 146.82 γ = 120
Symmetry Space Group P 32 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 MARMOSAIC 225 mm CCD 2008-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97881 SLS X10SA
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 20 99.8 0.053 26 11 30154 30110 4.3 35
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 1.8 1.9 99.9 0.377 4.3 6.8 4432
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 Rigid body refinement of native structure 2q0i in REFMAC5 THROUGHOUT 2Q0I 1.8 19.96 28614 1495 99.95 0.15809 0.15608 0.1709 0.19627 0.2079 RANDOM 25.648
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.109 r_dihedral_angle_4_deg 18.973 r_dihedral_angle_3_deg 14.552 r_dihedral_angle_1_deg 6.306 r_scangle_it 5.39 r_scbond_it 3.846 r_mcangle_it 2.275 r_angle_refined_deg 2.207 r_mcbond_it 1.931 r_angle_other_deg 1.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.109 r_dihedral_angle_4_deg 18.973 r_dihedral_angle_3_deg 14.552 r_dihedral_angle_1_deg 6.306 r_scangle_it 5.39 r_scbond_it 3.846 r_mcangle_it 2.275 r_angle_refined_deg 2.207 r_mcbond_it 1.931 r_angle_other_deg 1.139 r_mcbond_other 0.498 r_symmetry_vdw_other 0.389 r_symmetry_hbond_refined 0.363 r_symmetry_vdw_refined 0.273 r_nbd_refined 0.232 r_nbd_other 0.223 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.187 r_chiral_restr 0.155 r_nbtor_other 0.093 r_bond_refined_d 0.027 r_gen_planes_refined 0.012 r_metal_ion_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2378 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction XSCALE data scaling REFMAC phasing