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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 281 0.1M Tris-HCl pH 7.5, 2.20M (NH4)2HPO4, 10mM 2-aminobenzimidazole
Crystal Properties Matthews coefficient Solvent content 2.37 48.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.07 α = 90 b = 69.065 β = 90 c = 102.121 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 2017-05-02 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 1.6 57.22 96.9 0.071 10.8 5.2 55927
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 1.6 1.68 89.6 0.379 2.7 3.1
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 4DUH 1.6 57.21 53016 2762 96.23 0.22889 0.22822 0.2358 0.24166 0.245 RANDOM 23.039
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] -0.19 0.62 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.995 r_dihedral_angle_3_deg 12.655 r_dihedral_angle_4_deg 12.335 r_dihedral_angle_1_deg 5.582 r_long_range_B_refined 3.749 r_long_range_B_other 3.748 r_scangle_other 1.987 r_mcangle_it 1.657 r_mcangle_other 1.657 r_angle_refined_deg 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.995 r_dihedral_angle_3_deg 12.655 r_dihedral_angle_4_deg 12.335 r_dihedral_angle_1_deg 5.582 r_long_range_B_refined 3.749 r_long_range_B_other 3.748 r_scangle_other 1.987 r_mcangle_it 1.657 r_mcangle_other 1.657 r_angle_refined_deg 1.33 r_scbond_it 1.202 r_scbond_other 1.202 r_mcbond_it 0.969 r_mcbond_other 0.966 r_angle_other_deg 0.94 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_bond_other_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 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 2855 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing