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E. coli GyrB ATPase domain in complex with 4-nitropheno
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 2.34 47.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.811 α = 90 b = 67.519 β = 90 c = 102.493 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 0.979 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 1.8 56.38 99.7 0.081 0.088 0.034 6.4 6.5 39937
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 1.8 1.83 99.2 0.646 0.71 0.29 0.805 5.7
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 1.89 56.38 32328 1677 99.06 0.20944 0.20806 0.2159 0.23675 0.2411 RANDOM 35.124
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] -1.13 2.54 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.01 r_dihedral_angle_3_deg 14.754 r_dihedral_angle_4_deg 12.447 r_long_range_B_refined 5.566 r_long_range_B_other 5.558 r_scangle_other 3.875 r_angle_other_deg 3.784 r_mcangle_it 2.8 r_mcangle_other 2.799 r_dihedral_angle_1_deg 2.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.01 r_dihedral_angle_3_deg 14.754 r_dihedral_angle_4_deg 12.447 r_long_range_B_refined 5.566 r_long_range_B_other 5.558 r_scangle_other 3.875 r_angle_other_deg 3.784 r_mcangle_it 2.8 r_mcangle_other 2.799 r_dihedral_angle_1_deg 2.653 r_scbond_it 2.465 r_scbond_other 2.432 r_mcbond_it 1.911 r_mcbond_other 1.911 r_angle_refined_deg 1.579 r_chiral_restr 0.153 r_bond_refined_d 0.023 r_gen_planes_refined 0.005 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 2885 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing