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The structure of the S. aureus DnaG RNA Polymerase Domain bound to ATP and Manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E2K pdb entry 4E2K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 0.15M sodium thiocyanate, 0.1M Bis-Tris, 13% PEG3350, 2% Benzamidine, 2.5 mM ATP, 5 mM MnCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.38 63.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.261 α = 90 b = 151.261 β = 90 c = 38.665 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 ADSC QUANTUM 315r 2009-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.003 130.996 99.8 0.046 22.1 5.4 34568 34499
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 98.8 0.287 0.287 2.8 5.3 4915
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT pdb entry 4E2K 2.003 43.665 1.35 34480 1705 99.74 0.1633 0.1615 0.159 0.1969 0.1914 copied from 4E2K 34.795
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] 2.6171 2.6171 -5.2342
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.809 f_angle_d 1.062 f_chiral_restr 0.066 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2578 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 52
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction PHENIX phasing