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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 0.1M Tris-HCl pH 7.5, 2.20M (NH4)2HPO4, 10mM 2-aminobenzimidazole
Crystal Properties Matthews coefficient Solvent content 2.37 48.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.882 α = 90 b = 67.75 β = 90 c = 102.96 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 1.73 67.75 95.3 0.049 16.5 4.5 43503
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 1.73 1.77 0.523
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 4DUH 1.73 56.66 41311 2099 94.54 0.19788 0.19644 0.2025 0.22665 0.2348 RANDOM 30.584
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] 0.27 0.32 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.84 r_dihedral_angle_3_deg 12.502 r_dihedral_angle_4_deg 7.073 r_long_range_B_other 6.362 r_long_range_B_refined 6.361 r_scangle_other 5.757 r_dihedral_angle_1_deg 5.372 r_scbond_it 4.512 r_scbond_other 4.51 r_mcangle_other 4.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.84 r_dihedral_angle_3_deg 12.502 r_dihedral_angle_4_deg 7.073 r_long_range_B_other 6.362 r_long_range_B_refined 6.361 r_scangle_other 5.757 r_dihedral_angle_1_deg 5.372 r_scbond_it 4.512 r_scbond_other 4.51 r_mcangle_other 4.015 r_mcangle_it 4.013 r_angle_other_deg 3.528 r_mcbond_it 3.37 r_mcbond_other 3.355 r_angle_refined_deg 1.187 r_chiral_restr 0.052 r_bond_refined_d 0.007 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_other_d 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 2875 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling MOLREP phasing