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N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM NaCl condition
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 8 291 15-25% PEG 3350, 2 mM MgCl2, 100 mM Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.84 56.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.91 α = 90 b = 140.88 β = 90 c = 79.52 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 PIXEL DECTRIS PILATUS 6M 2012-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.033 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 27.49 99.9 0.062 0.026 0.999 22.4 6.5 39031
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 1.9 1.95 99.8 1.114 0.484 0.643 2.5 6.2 2860
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 1.9 27.49 37010 2020 99.83 0.1854 0.1835 0.19 0.2198 0.2209 RANDOM 35.761
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] -1.17 1.73 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.88 r_dihedral_angle_4_deg 17.9 r_dihedral_angle_3_deg 12.709 r_dihedral_angle_1_deg 5.167 r_mcangle_it 1.794 r_angle_refined_deg 1.256 r_mcbond_it 1.186 r_mcbond_other 1.184 r_angle_other_deg 0.754 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.88 r_dihedral_angle_4_deg 17.9 r_dihedral_angle_3_deg 12.709 r_dihedral_angle_1_deg 5.167 r_mcangle_it 1.794 r_angle_refined_deg 1.256 r_mcbond_it 1.186 r_mcbond_other 1.184 r_angle_other_deg 0.754 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2923 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction XDS data reduction