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Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KZN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 296 40-43% MPD_P1K_P3350, 100 mM Mops/Na-Hepes, 100 mM Divalents
Crystal Properties Matthews coefficient Solvent content 2.11 41.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.91 α = 90 b = 55.86 β = 100.62 c = 51.46 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315 2010-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 26.64 94.7 0.045 0.063 0.043 10.4 1.9 60328
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 94.6 0.345 0.345 0.331 2.2 1.9 8753
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 1KZN 1.5 26.64 57219 3103 94.38 0.1689 0.1673 0.1665 0.1979 0.1978 RANDOM 19.947
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] 0.3 -0.1 -0.96 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.816 r_dihedral_angle_4_deg 20.224 r_dihedral_angle_3_deg 13.07 r_dihedral_angle_1_deg 5.702 r_mcangle_it 2.751 r_angle_refined_deg 2.23 r_mcbond_it 1.915 r_mcbond_other 1.909 r_angle_other_deg 1.07 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.816 r_dihedral_angle_4_deg 20.224 r_dihedral_angle_3_deg 13.07 r_dihedral_angle_1_deg 5.702 r_mcangle_it 2.751 r_angle_refined_deg 2.23 r_mcbond_it 1.915 r_mcbond_other 1.909 r_angle_other_deg 1.07 r_chiral_restr 0.136 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3046 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction