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Extremely 'open' clamp structure of DNA gyrase: role of the Corynebacteriales GyrB specific insert
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IFZ 3IFZ, 3IG0, 3ZKB experimental model PDB 3IG0 3IFZ, 3IG0, 3ZKB experimental model PDB 3ZKB 3IFZ, 3IG0, 3ZKB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 100 mM Sodium Acetate
100 mM MES pH 6.5
26% PEG 400
25% EG
10 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 3 59.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.523 α = 75.64 b = 96.782 β = 64.44 c = 105.791 γ = 65.8
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 2015-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.950 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 3.3 48.35 98.2 0.236 0.99 7 3.99 44305 86.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 3IFZ, 3IG0, 3ZKB 3.3 48.35 44284 2235 98.1 0.177 0.173 0.1893 0.251 0.2662 RANDOM 100
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] 0.8116 9.8608 0.0306 -1.1871 17.1963 0.3755
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.5 t_omega_torsion 2.53 t_angle_deg 1.22 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.5 t_omega_torsion 2.53 t_angle_deg 1.22 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16808 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose BUSTER refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction