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Crystal structure of the Vibrio cholera VqmA-Ligand-DNA complex provides molecular mechanisms for drug design
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 301 3.85% polyethylene glycol (PEG) 3350 and 0.165 M K2HPO4/NaH2PO4 pH 7.5
Crystal Properties Matthews coefficient Solvent content 4.48 72.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.78 α = 90 b = 108.98 β = 90 c = 214.32 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M 2018-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.51 53.58 99.7 0.073 0.077 0.021 0.998 18.9 13.1 43223
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.51 2.58 99.8 1.675 1.743 0.475 0.79 13.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 2.51 43.326 1.34 43108 1997 99.62 0.1932 0.1915 0.1954 0.2294 0.2328 96.4558
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3575 Nucleic Acid Atoms 732 Solvent Atoms 6 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement Aimless data scaling CRANK2 phasing PDB_EXTRACT data extraction xia2 data reduction