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Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EHI PDB ENTRY 1EHI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.15 42.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.73 α = 90 b = 66.082 β = 96.57 c = 78.789 γ = 90
Symmetry Space Group P 1 21 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 210 mirrors 2001-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.19 79 94.1 0.052 0.052 21.5 5.5 33377 33377 32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.25 76.3 0.177 0.177 3.81 3.5 1752
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EHI 2.19 79.06 31696 1667 93.74 0.191 0.18786 0.25063 0.2006 RANDOM 32.009
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] 0.35 0.27 0.71 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.565 r_dihedral_angle_4_deg 20.331 r_dihedral_angle_3_deg 17.784 r_dihedral_angle_1_deg 7.234 r_scangle_it 3.475 r_scbond_it 2.364 r_angle_refined_deg 1.715 r_mcangle_it 1.517 r_mcbond_it 1.22 r_angle_other_deg 0.864
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.565 r_dihedral_angle_4_deg 20.331 r_dihedral_angle_3_deg 17.784 r_dihedral_angle_1_deg 7.234 r_scangle_it 3.475 r_scbond_it 2.364 r_angle_refined_deg 1.715 r_mcangle_it 1.517 r_mcbond_it 1.22 r_angle_other_deg 0.864 r_xyhbond_nbd_other 0.359 r_symmetry_vdw_other 0.229 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.222 r_mcbond_other 0.217 r_nbtor_refined 0.188 r_nbd_other 0.187 r_xyhbond_nbd_refined 0.172 r_symmetry_vdw_refined 0.165 r_chiral_restr 0.104 r_nbtor_other 0.092 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5496 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection