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Ternary complex of Staphylococcus aureus DNA gyrase with AMK12 and DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 NULL
Crystal Properties Matthews coefficient Solvent content 2.98 58.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.592 α = 90 b = 92.592 β = 90 c = 405.464 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 PIXEL DECTRIS EIGER2 X 16M 2019-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 81.09 100 0.193 0.198 0.043 0.998 11.7 20.2 86845 41.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 99.5 2.017 2.085 0.52 0.557 15.6
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 FOURIER SYNTHESIS THROUGHOUT 2XCS 2.3 80.32 82229 4484 99.92 0.181 0.179 0.1847 0.2167 0.2218 RANDOM 45.492
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] -0.53 -0.27 -0.53 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.192 r_dihedral_angle_4_deg 17.822 r_dihedral_angle_3_deg 15.068 r_dihedral_angle_1_deg 6.675 r_angle_refined_deg 1.636 r_angle_other_deg 1.358 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.192 r_dihedral_angle_4_deg 17.822 r_dihedral_angle_3_deg 15.068 r_dihedral_angle_1_deg 6.675 r_angle_refined_deg 1.636 r_angle_other_deg 1.358 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10548 Nucleic Acid Atoms 801 Solvent Atoms 347 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction DIALS data reduction REFMAC phasing