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Crystal structure of Shewanella oneidensis NrtR complexed with a 27mer DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GZ5 PDB entry 3GZ5
Crystallization Crystal Properties Matthews coefficient Solvent content 3.78 67.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.58 α = 90 b = 159.58 β = 90 c = 73.067 γ = 120
Symmetry Space Group P 32 1 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2008-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER
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 2.9 50 98.4 0.097 20.684 6.1 23259
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 2.9 3 97.9 0.478 6.2
Refinement Statistics Diffraction ID Structure Solution 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 PDB entry 3GZ5 2.901 33.217 1.37 23248 1199 98.55 0.1777 0.174 0.1662 0.2472 0.2412 36.623
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.159 f_angle_d 1.338 f_chiral_restr 0.067 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3510 Nucleic Acid Atoms 1109 Solvent Atoms 73 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction