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Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a fragment
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 2.05 40.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.32 α = 90 b = 56.079 β = 98.99 c = 50.183 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 PIXEL DECTRIS PILATUS 2M 2012-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9173 Diamond I04-1
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 1.475 27.499 89.9 0.037 0.05 0.028 11 2.9 58540 58540
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 1.48 1.51 56.2 0.394 0.394 0.296 1.9 2.1 2678
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 1.48 27.5 55576 2961 89.66 0.2187 0.2162 0.2216 0.264 0.2658 RANDOM 27.734
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] -0.73 -1.82 1.04 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.572 r_dihedral_angle_4_deg 16.748 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_1_deg 6.2 r_mcangle_it 3.641 r_mcbond_it 2.624 r_mcbond_other 2.622 r_angle_refined_deg 1.964 r_angle_other_deg 1.086 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.572 r_dihedral_angle_4_deg 16.748 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_1_deg 6.2 r_mcangle_it 3.641 r_mcbond_it 2.624 r_mcbond_other 2.622 r_angle_refined_deg 1.964 r_angle_other_deg 1.086 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3093 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction