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2.3 A structure of the NBTI B1 with S. aureus DNA gyrase and double-nicked DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other model from previous experiment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M MES pH 6.5, 15 % (w/v) PEG 6000, 5 % (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 2.96 58.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.706 α = 90 b = 92.706 β = 90 c = 401.766 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 XE 16M 2025-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953731 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 80.35 100 0.222 0.238 0.087 0.996 8.2 14.9 86337
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) 2.3 2.34 100 1.382 1.483 0.534 0.684 1.2 15.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 80.286 86192 4382 100 0.216 0.2135 0.2134 0.2524 0.2521 RANDOM 43.763
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] 0.383 0.192 0.383 -1.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.668 r_dihedral_angle_6_deg 14.448 r_dihedral_angle_2_deg 8.356 r_lrange_it 7.338 r_dihedral_angle_1_deg 6.714 r_scangle_it 5.667 r_mcangle_it 3.914 r_scbond_it 3.821 r_mcbond_it 2.579 r_angle_refined_deg 1.786
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.668 r_dihedral_angle_6_deg 14.448 r_dihedral_angle_2_deg 8.356 r_lrange_it 7.338 r_dihedral_angle_1_deg 6.714 r_scangle_it 5.667 r_mcangle_it 3.914 r_scbond_it 3.821 r_mcbond_it 2.579 r_angle_refined_deg 1.786 r_nbtor_refined 0.305 r_symmetry_xyhbond_nbd_refined 0.223 r_nbd_refined 0.21 r_symmetry_nbd_refined 0.185 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.134 r_ncsr_local_group_1 0.082 r_ncsr_local_group_2 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10412 Nucleic Acid Atoms 798 Solvent Atoms 236 Heterogen Atoms 118
Software Software Software Name Purpose gemmi data extraction DIALS data reduction Aimless data scaling REFMAC refinement PHASER phasing