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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 41.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.539 α = 90 b = 55.556 β = 99.73 c = 51.113 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 IMAGE PLATE RIGAKU RAXIS IV++ 2009-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.05 38.2 96.8 0.098 7.5 3.73 24461
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 2.05 2.12 97.2 0.522 2 3.72 2438
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 2.05 38.2 23258 1201 96.79 0.2109 0.2083 0.217 0.2569 0.2588 RANDOM 43.9
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] 0.28 -1.18 -0.81 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.836 r_dihedral_angle_4_deg 19.776 r_dihedral_angle_3_deg 15.768 r_dihedral_angle_1_deg 6.696 r_mcangle_it 4.546 r_mcbond_other 3.267 r_mcbond_it 3.266 r_angle_refined_deg 1.977 r_angle_other_deg 1.024 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.836 r_dihedral_angle_4_deg 19.776 r_dihedral_angle_3_deg 15.768 r_dihedral_angle_1_deg 6.696 r_mcangle_it 4.546 r_mcbond_other 3.267 r_mcbond_it 3.266 r_angle_refined_deg 1.977 r_angle_other_deg 1.024 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3050 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling MOLREP phasing PDB_EXTRACT data extraction