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Bacterial GyrB ATPase domain in complex with a chemical fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DUH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 281 0.1 M Tris-HCl pH 7.5, 2.20 M (NH4)2HPO4, 10 mM 2-aminobenzimidazole
Crystal Properties Matthews coefficient Solvent content 2.37 48.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.576 α = 90 b = 68.007 β = 90 c = 102.877 γ = 90
Symmetry Space Group P 21 21 21
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 2017-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
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 50 99.8 0.099 34.7 5 29857
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 2.07 0.428
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4DUH 2 50 28335 1468 99.11 0.18804 0.18634 0.22093 0.2294 RANDOM 25.359
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] -0.67 1.6 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.742 r_dihedral_angle_3_deg 12.048 r_dihedral_angle_4_deg 7.758 r_dihedral_angle_1_deg 5.434 r_long_range_B_refined 4.561 r_long_range_B_other 4.56 r_scangle_other 2.755 r_mcangle_it 2.371 r_mcangle_other 2.371 r_scbond_it 1.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.742 r_dihedral_angle_3_deg 12.048 r_dihedral_angle_4_deg 7.758 r_dihedral_angle_1_deg 5.434 r_long_range_B_refined 4.561 r_long_range_B_other 4.56 r_scangle_other 2.755 r_mcangle_it 2.371 r_mcangle_other 2.371 r_scbond_it 1.664 r_scbond_other 1.663 r_mcbond_it 1.479 r_mcbond_other 1.473 r_angle_refined_deg 1.316 r_angle_other_deg 0.929 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2884 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling MOLREP phasing