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Apo structure of 55 kDa N-terminal domain of E. coli DNA gyrase A subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y3P PDB ENTRY 2Y3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.96 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.57 α = 105.16 b = 95.53 β = 118.81 c = 95.89 γ = 103.42
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 PILATUS 6M 2012-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
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 1.9 81.51 97 0.07 11 2.9 194509 23.6
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 1.9 1.95 94.7 0.49 2.7 2.6
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 PDB ENTRY 2Y3P 1.9 81.51 184697 9799 96.97 0.17031 0.16935 0.1759 0.18859 0.1936 RANDOM 32.3
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] 0.13 0.06 0.59 0.22 0.4 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.591 r_dihedral_angle_4_deg 16.352 r_dihedral_angle_3_deg 12.418 r_dihedral_angle_1_deg 5.218 r_scbond_it 2.244 r_mcangle_it 1.871 r_angle_refined_deg 1.502 r_angle_other_deg 1.312 r_mcbond_it 1.228 r_mcbond_other 1.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.591 r_dihedral_angle_4_deg 16.352 r_dihedral_angle_3_deg 12.418 r_dihedral_angle_1_deg 5.218 r_scbond_it 2.244 r_mcangle_it 1.871 r_angle_refined_deg 1.502 r_angle_other_deg 1.312 r_mcbond_it 1.228 r_mcbond_other 1.228 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15016 Nucleic Acid Atoms Solvent Atoms 1056 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing