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A domain insertion in E. coli GyrB adopts a novel fold that plays a critical role in gyrase function
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AB4 The structure was solved as a combination of MR and SAD method. The starting model used corresponds to PDB ID 1AB4.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 8 291 90 mM imidazole pH 8.0, 11% isopropanol, 18 mM magnesium chloride, 10 mM spermidine, 3% pentaerythritol ethoxylate 15/4, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.56 52.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.062 α = 90 b = 147.493 β = 90 c = 138.87 γ = 90
Symmetry Space Group C 2 2 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 ADSC Q315r 2008-07-22 SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97920 APS 24-ID-E
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 3.1 35.6 99.6 0.103 5 20320 56.37
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.1 3.2 99.6 0.387 3.8 4.6
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 MR-SAD The structure was solved as a combination of MR and SAD method. The starting model used corresponds to PDB ID 1AB4. 3.103 35.6 1.9 38496 3778 99.26 0.238 0.234 0.231 0.282 0.2805 82.602
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] 41.129 -21.17 -19.959
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.64 f_angle_d 0.618 f_chiral_restr 0.042 f_bond_d 0.003 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6666 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction