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2.55 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-493) of DNA Topoisomerase IV Subunit A from Pseudomonas putida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Protein: 9.5 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: Classics II (C1), 3.5M Sodium formate pH (7.0); Cryo: 4.0M Sodium formate
Crystal Properties Matthews coefficient Solvent content 4.16 70.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.494 α = 90 b = 224.057 β = 90 c = 115.747 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 100 CCD MARMOSAIC 300 mm CCD C(111) 2017-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.55 30 99 0.068 0.068 0.074 0.027 28.3 7.4 30230 -3 70.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.59 98.8 0.785 0.785 0.848 0.316 0.903 2.2 6.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5EIX 2.55 29.35 28738 1487 98.4 0.20958 0.20765 0.24654 0.2455 RANDOM 95.211
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] 10.4 -8.77 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.992 r_dihedral_angle_4_deg 10.486 r_dihedral_angle_3_deg 9.379 r_long_range_B_refined 7.329 r_long_range_B_other 7.326 r_scangle_other 4.965 r_mcangle_it 4.814 r_mcangle_other 4.814 r_scbond_it 3.091 r_scbond_other 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.992 r_dihedral_angle_4_deg 10.486 r_dihedral_angle_3_deg 9.379 r_long_range_B_refined 7.329 r_long_range_B_other 7.326 r_scangle_other 4.965 r_mcangle_it 4.814 r_mcangle_other 4.814 r_scbond_it 3.091 r_scbond_other 3.09 r_mcbond_it 3.021 r_mcbond_other 3.003 r_dihedral_angle_1_deg 2.071 r_angle_refined_deg 1.41 r_angle_other_deg 0.89 r_chiral_restr 0.08 r_gen_planes_refined 0.023 r_gen_planes_other 0.02 r_bond_refined_d 0.008 r_bond_other_d 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 3627 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing