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Activated form of VanR from S. coelicolor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UIC 5UIC, 1KGS experimental model PDB 1KGS 5UIC, 1KGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 298 Protein stock (11.3 mg/mL in 500 mM NaCl, 5 mM MgCl2, 10% glycerol, 40 mM Tris pH 8) was mixed 10:1 (v/v) with 50 mM BeSO4, 350 mM NaF, and 70 mM MgCl2. 0.5 uL of this solution was mixed with an equal volume of 2.5 M NaCl, 0.1 M Tris pH 7, 0.2 M MgCl2 and incubated under Al's Oil
Crystal Properties Matthews coefficient Solvent content 3.25 62.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.37 α = 90 b = 97.37 β = 90 c = 118.65 γ = 120
Symmetry Space Group P 65 2 2
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 9M 2019-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920091 NSLS-II 17-ID-1
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 2.03 28.85 97.5 0.052 0.059 0.028 0.998 15.3 4.4 21574 42.4
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 2.03 2.1 0.406 0.463 0.145 0.916 3.5
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5UIC, 1KGS 2.03 28.85 20485 1077 97.45 0.182 0.1825 0.222 0.2223 random 41.4075
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 1674 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 5
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction