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Acinetobacter baumannii DNA gyrase B 23kDa ATPase subdomain complexed with EBL2888
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PQI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 NULL
Crystal Properties Matthews coefficient Solvent content 2.2 44.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.634 α = 90 b = 48.293 β = 123.85 c = 82.692 γ = 90
Symmetry Space Group C 1 2 1
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 2021-02-11 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 1.55 43.5 99.9 0.105 0.11 0.033 0.999 8.9 10.9 57543 18.6
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 1.55 1.58 99 1.55 1.625 0.482 0.66 11.1
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 7PQI 1.55 43.54 54572 2969 99.94 0.1823 0.18 0.1879 0.2235 0.2291 RANDOM 31.638
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] 3.33 2.55 -5.57 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.193 r_dihedral_angle_4_deg 14.2 r_dihedral_angle_3_deg 12.364 r_rigid_bond_restr 6.718 r_dihedral_angle_1_deg 5.782 r_angle_other_deg 1.341 r_angle_refined_deg 1.235 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.193 r_dihedral_angle_4_deg 14.2 r_dihedral_angle_3_deg 12.364 r_rigid_bond_restr 6.718 r_dihedral_angle_1_deg 5.782 r_angle_other_deg 1.341 r_angle_refined_deg 1.235 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2892 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 65
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction PHASER phasing