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Crystal structure of an anti-activation complex in bacterial quorum sensing
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L3L PDB entry 1L3L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 1 mM DTT, 60 mM HEPES, 120 mM CaCl2, 16.8% PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.76 55.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.9 α = 94.87 b = 62.48 β = 110.45 c = 65.5 γ = 99.17
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD NOIR-1 Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror 2005-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.127 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 40 96.7 0.088 0.088 5.4 1.96 55752 53940 5 5 19.8
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 2.07 96.7 0.464 1.3 1.96 5580
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 (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 1L3L 2 39.85 55735 53915 2694 96.6 0.235 0.235 0.2368 0.276 0.2767 RANDOM 40
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] -5.35 0.86 6.8 -3.77 -1.63 9.12
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.3 c_scangle_it 3.59 c_scbond_it 2.43 c_mcangle_it 2.31 c_mcbond_it 1.43 c_angle_deg 1.2 c_improper_angle_d 0.83 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5050 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 34
Software Software Software Name Purpose CNS refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling PHASER phasing