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The 2.1A crystal structure of S. aureus Gyrase complex with GSK299423 and DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XCQ PDB ENTRY 2XCQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 18% PEG 5000MME, 0.1 M BISTRIS PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.92 57.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.318 α = 90 b = 93.318 β = 90 c = 412.812 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.1 30 98.6 0.12 11.4 5 113168 28.25
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 2.1 2.21 98.6 0.45 2.6 4.3
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 PDB ENTRY 2XCQ 2.1 20 113168 2907 100 0.18373 0.18295 0.1862 0.21379 0.2184 RANDOM 38.417
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] -0.34 -0.17 -0.34 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.817 r_dihedral_angle_4_deg 14.052 r_dihedral_angle_3_deg 9.558 r_scangle_it 3.576 r_dihedral_angle_1_deg 2.563 r_scbond_it 2.362 r_mcangle_it 1.519 r_angle_refined_deg 1.268 r_mcbond_it 0.748 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.817 r_dihedral_angle_4_deg 14.052 r_dihedral_angle_3_deg 9.558 r_scangle_it 3.576 r_dihedral_angle_1_deg 2.563 r_scbond_it 2.362 r_mcangle_it 1.519 r_angle_refined_deg 1.268 r_mcbond_it 0.748 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10606 Nucleic Acid Atoms 800 Solvent Atoms 826 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing