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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 VAPOR DIFFUSION, SITTING DROP 285 0.1M Tris-HCl pH 7.5, 2.20M (NH4)2HPO4, 10mM 2-aminobenzimidazole
Crystal Properties Matthews coefficient Solvent content 2.38 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.379 α = 90 b = 68.558 β = 90 c = 102.701 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 1.8 57.02 97.9 0.063 40.4 4.9 39968
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 1.8 1.86 99.3 0.374 5.4
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 1.8 57.02 37995 1922 97.77 0.19568 0.1943 0.2031 0.22222 0.2296 RANDOM 25.923
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] -0.76 1.2 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.771 r_dihedral_angle_3_deg 11.159 r_dihedral_angle_4_deg 9.728 r_dihedral_angle_1_deg 5.26 r_long_range_B_refined 3.742 r_long_range_B_other 3.742 r_scangle_other 2.007 r_mcangle_it 1.575 r_mcangle_other 1.574 r_angle_refined_deg 1.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.771 r_dihedral_angle_3_deg 11.159 r_dihedral_angle_4_deg 9.728 r_dihedral_angle_1_deg 5.26 r_long_range_B_refined 3.742 r_long_range_B_other 3.742 r_scangle_other 2.007 r_mcangle_it 1.575 r_mcangle_other 1.574 r_angle_refined_deg 1.307 r_scbond_it 1.207 r_scbond_other 1.206 r_angle_other_deg 0.934 r_mcbond_other 0.922 r_mcbond_it 0.921 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 2856 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling MOLREP phasing