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Quorum Sensing Control Repressor, QscR, Bound to N-3-oxo-dodecanoyl-L-Homoserine Lactone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SCRWL MODEL OF AHL AND DNA-BINDING DOMAINS OF TRAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.83 277 0.168 M magnesium acetate, 21.8% PEG8000, 0.1 M Tris, pH 7.83, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.862 α = 90 b = 94.862 β = 90 c = 104.953 γ = 120
Symmetry Space Group P 31 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 NOIR-1 2009-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0000 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 25 100 0.052 0.052 40 11.9 19230 19230 61.9
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 2.5 2.59 99.6 0.41 4.8 12.2 1882
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SCRWL MODEL OF AHL AND DNA-BINDING DOMAINS OF TRAR 2.55 15 17116 17116 953 99.58 0.2249 0.2249 0.22264 0.2322 0.26594 0.2711 RANDOM 78.553
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] -0.39 -0.19 -0.39 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.967 r_dihedral_angle_4_deg 15.115 r_dihedral_angle_3_deg 13.946 r_dihedral_angle_1_deg 4.14 r_mcangle_it 2.416 r_scangle_it 1.621 r_mcbond_it 1.573 r_angle_refined_deg 1.295 r_scbond_it 1.117 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.967 r_dihedral_angle_4_deg 15.115 r_dihedral_angle_3_deg 13.946 r_dihedral_angle_1_deg 4.14 r_mcangle_it 2.416 r_scangle_it 1.621 r_mcbond_it 1.573 r_angle_refined_deg 1.295 r_scbond_it 1.117 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3608 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 43
Software Software Software Name Purpose Blu-Ice data collection JBluIce-EPICS data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling