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Crystal structure of the DNA-binding domains of YvoA in complex with palindromic operator DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WV0 DNA-binding domain of PDB entry 2wv0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292.15 50 mM sodium cacodylate,
200 mM sodium citrate,
10 mM MgCl2,
5 % (v/v) isopropanol
Crystal Properties Matthews coefficient Solvent content 2.39 48.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.554 α = 90 b = 48.554 β = 90 c = 153.941 γ = 120
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 RAYONIX MX-225 2010-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.91 32.52 99.8 0.085 10.61 3.8 31230 25.86
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 1.91 1.98 98.7 0.87 1.9 3.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE DNA-binding domain of PDB entry 2wv0 1.91 32.52 1.95 31190 1558 99.67 0.1809 0.1783 0.1803 0.2294 0.2273 Random selection 29.8537
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 19.676 f_angle_d 1.087 f_chiral_restr 0.046 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2420 Nucleic Acid Atoms 614 Solvent Atoms 287 Heterogen Atoms 2
Software Software Software Name Purpose XDS data reduction PHASER phasing PHENIX refinement