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E. coli GyrB ATPase domain in complex with methyl 3,4-dihydroxybenzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Z9B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M Tris-HCl pH 7.5, 2.20 M (NH4)2HPO4, 10 mM 2-aminobenzimidazole
Crystal Properties Matthews coefficient Solvent content 2.54 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.973 α = 90 b = 67.389 β = 90 c = 102.365 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 PIXEL DECTRIS EIGER X 16M 2018-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97907 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.75 56.29 99.9 0.069 0.075 0.029 6.4 6.5 43063
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 1.75 1.78 100 0.469 0.511 0.2 0.903 6.4
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 5Z9B 1.75 56.29 40825 2179 99.73 0.22605 0.22463 0.2316 0.25235 0.2604 RANDOM 27.229
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 1.55 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.545 r_dihedral_angle_3_deg 13.656 r_dihedral_angle_4_deg 10.551 r_dihedral_angle_1_deg 4.001 r_angle_other_deg 3.68 r_long_range_B_refined 2.319 r_long_range_B_other 2.266 r_angle_refined_deg 1.258 r_mcangle_it 1.044 r_mcangle_other 1.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.545 r_dihedral_angle_3_deg 13.656 r_dihedral_angle_4_deg 10.551 r_dihedral_angle_1_deg 4.001 r_angle_other_deg 3.68 r_long_range_B_refined 2.319 r_long_range_B_other 2.266 r_angle_refined_deg 1.258 r_mcangle_it 1.044 r_mcangle_other 1.044 r_scangle_other 0.89 r_mcbond_it 0.574 r_mcbond_other 0.574 r_scbond_other 0.537 r_scbond_it 0.535 r_chiral_restr 0.082 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 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 2887 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing