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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 code 1EHI
Crystallization Crystal Properties Matthews coefficient Solvent content 2.12 42.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.661 α = 90 b = 66.408 β = 96.24 c = 78.59 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 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 79 99.7 0.038 26.9 3.7 46823 46823 37.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.162 4.5 3.8 3276
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB code 1EHI 2 79.06 46823 44470 2336 99.62 0.20187 0.1998 0.2117 0.24148 0.2058 RANDOM 37.837
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] -0.07 0.01 0.27 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.448 r_dihedral_angle_4_deg 17.457 r_dihedral_angle_3_deg 16.746 r_dihedral_angle_1_deg 7.33 r_scangle_it 4.256 r_scbond_it 3.074 r_angle_refined_deg 1.991 r_mcangle_it 1.933 r_mcbond_it 1.567 r_angle_other_deg 1.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.448 r_dihedral_angle_4_deg 17.457 r_dihedral_angle_3_deg 16.746 r_dihedral_angle_1_deg 7.33 r_scangle_it 4.256 r_scbond_it 3.074 r_angle_refined_deg 1.991 r_mcangle_it 1.933 r_mcbond_it 1.567 r_angle_other_deg 1.034 r_mcbond_other 0.357 r_symmetry_hbond_refined 0.278 r_symmetry_vdw_refined 0.248 r_nbd_refined 0.23 r_symmetry_vdw_other 0.221 r_nbd_other 0.206 r_nbtor_refined 0.194 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.128 r_nbtor_other 0.097 r_bond_refined_d 0.024 r_xyhbond_nbd_other 0.013 r_gen_planes_refined 0.008 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 5479 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement