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Crystal Structure of GyraseB N-Terminal Domain complex with ATP from Salmonella Typhi at 2.2A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EI1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M Lithium chloride
0.05M Bis Tris
12% PEG MME
Crystal Properties Matthews coefficient Solvent content 2.82 56.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.112 α = 90 b = 140.545 β = 90 c = 79.105 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS PILATUS3 2M 2018-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 39.58 99.5 0.134 0.17 0.103 0.993 8.9 4.76 24907 24.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 99.4 0.8 0.621 0.795 2 4.9
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 1EI1 2.2 39.58 23623 1249 99.3 0.17661 0.17442 0.1807 0.21666 0.2208 RANDOM 30.489
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] -2.14 3.33 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.393 r_dihedral_angle_4_deg 21.721 r_dihedral_angle_3_deg 16.33 r_long_range_B_refined 7.54 r_long_range_B_other 7.54 r_dihedral_angle_1_deg 6.277 r_scangle_other 4.697 r_mcangle_it 3.499 r_mcangle_other 3.498 r_scbond_it 3.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.393 r_dihedral_angle_4_deg 21.721 r_dihedral_angle_3_deg 16.33 r_long_range_B_refined 7.54 r_long_range_B_other 7.54 r_dihedral_angle_1_deg 6.277 r_scangle_other 4.697 r_mcangle_it 3.499 r_mcangle_other 3.498 r_scbond_it 3.033 r_scbond_other 3.033 r_mcbond_other 2.299 r_mcbond_it 2.298 r_angle_refined_deg 1.533 r_angle_other_deg 1.347 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 3008 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing