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E. coli GyrB ATPase domain in complex with Naringenin
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 51.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.584 α = 90 b = 67.499 β = 90 c = 103.752 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 2019-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.78 56.58 99.4 0.992 25.555 6.6 41802
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.84 0.96
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 1.78 56.58 39584 2160 99.25 0.23386 0.23218 0.2367 0.26564 0.2727 RANDOM 30.951
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] -0.61 1.23 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.781 r_dihedral_angle_3_deg 10.338 r_dihedral_angle_4_deg 7.644 r_dihedral_angle_1_deg 4.774 r_angle_other_deg 3.782 r_long_range_B_refined 3.691 r_long_range_B_other 3.386 r_mcangle_it 1.255 r_mcangle_other 1.254 r_angle_refined_deg 1.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.781 r_dihedral_angle_3_deg 10.338 r_dihedral_angle_4_deg 7.644 r_dihedral_angle_1_deg 4.774 r_angle_other_deg 3.782 r_long_range_B_refined 3.691 r_long_range_B_other 3.386 r_mcangle_it 1.255 r_mcangle_other 1.254 r_angle_refined_deg 1.098 r_scangle_other 0.998 r_mcbond_it 0.692 r_mcbond_other 0.692 r_scbond_other 0.573 r_scbond_it 0.572 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_gen_planes_other 0.002 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 2968 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing