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Crystal Structure of the Ternary Complex of AgrE with Ornithine and NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295.15 sodium acetate, sodium citrate (pH5.5), PEG4000, glycerol
Crystal Properties Matthews coefficient Solvent content 2.99 58.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.895 α = 90 b = 201.141 β = 90 c = 99.436 γ = 90
Symmetry Space Group C 2 2 21
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 270 2019-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.979 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.4 50 99 0.967 9.77 5.8 71345 28.6547168205
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 0.535
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6LRF 2.4121811586 46.7322103795 1.32630767749 71292 2007 98.6289999032 0.193120163194 0.19145144531 0.1968 0.250967979569 0.2555 33.2448740933
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 f_dihedral_angle_d 15.1088944142 f_angle_d 1.17623137181 f_chiral_restr 0.0458139940673 f_bond_d 0.00884077499565 f_plane_restr 0.00524414116164
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10605 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 62
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing PHENIX refinement