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Crystal Structure of a Putative GAF sensor protein from Burkholderia vietnamiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KSF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 290 BuviA.00048.a.B1.PS02344 at 57.5 mg/ml was mixed 1:1 with JCSG+(c1): 20% PEG-8000, 100 mM sodium phosphate dibasic/ citric acid, pH = 4.2, 200 mM NaCl, and cryoprotected with 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.07 40.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.46 α = 90 b = 70.2 β = 90 c = 103.07 γ = 90
Symmetry Space Group P 2 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 CCD MARMOSAIC 300 mm CCD Beryllium Lenses 2015-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.849 50 99.4 0.058 0.063 19.82 5.8 28101 -3 23.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.849 1.9 100 0.604 0.664 3.23 5.8
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 3KSF 1.8499 22.819 1.36 28073 1387 99.32 0.173 0.1709 0.1722 0.2135 0.2143 34.3893
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 13.28 f_angle_d 0.711 f_chiral_restr 0.048 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 12
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MoRDa phasing