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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 298 0.1M MES pH 6.0, 2.5M MgSO4, 8mM Tris-(2-carboxyethyl)phosphine (TECP).
Crystal Properties Matthews coefficient Solvent content 5.72 78.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.38 α = 90 b = 101.79 β = 90 c = 104.86 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 2017-03-09 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 2.74 73.04 93.1 0.071 17.4 5.5 27942
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 2.74 2.88 95.1 0.399 4.5 5.6
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 2.74 73.04 24332 1368 91.98 0.20048 0.1996 0.1998 0.21697 0.2205 RANDOM 57.309
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] -2.15 3.77 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.537 r_dihedral_angle_3_deg 12.944 r_dihedral_angle_4_deg 8.367 r_long_range_B_refined 7.41 r_long_range_B_other 7.254 r_dihedral_angle_1_deg 5.532 r_scangle_other 4.792 r_angle_other_deg 3.811 r_mcangle_it 3.795 r_mcangle_other 3.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.537 r_dihedral_angle_3_deg 12.944 r_dihedral_angle_4_deg 8.367 r_long_range_B_refined 7.41 r_long_range_B_other 7.254 r_dihedral_angle_1_deg 5.532 r_scangle_other 4.792 r_angle_other_deg 3.811 r_mcangle_it 3.795 r_mcangle_other 3.794 r_scbond_it 3.136 r_scbond_other 2.818 r_mcbond_it 2.264 r_mcbond_other 2.262 r_angle_refined_deg 1.226 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_gen_planes_other 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 2828 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing