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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 2I87 PDB ENTRY 2I87
Crystallization Crystal Properties Matthews coefficient Solvent content 2.16 42.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.802 α = 90 b = 66.972 β = 96.05 c = 78.992 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 mirror 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 2.46 79 99 0.07 0.07 23.9 3.7 25017 23741 40
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 2.5 2.59 99.2 0.621 0.621 2 3.7 1329
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2I87 2.46 47.51 25017 23741 1254 97.18 0.21283 0.20988 0.2174 0.26926 0.2038 RANDOM 45.406
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] 2.43 -1.44 -2.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.023 r_dihedral_angle_4_deg 21.081 r_dihedral_angle_3_deg 19.356 r_dihedral_angle_1_deg 7.761 r_scangle_it 3 r_scbond_it 2.019 r_angle_refined_deg 1.776 r_mcangle_it 1.262 r_mcbond_it 1.049 r_angle_other_deg 0.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.023 r_dihedral_angle_4_deg 21.081 r_dihedral_angle_3_deg 19.356 r_dihedral_angle_1_deg 7.761 r_scangle_it 3 r_scbond_it 2.019 r_angle_refined_deg 1.776 r_mcangle_it 1.262 r_mcbond_it 1.049 r_angle_other_deg 0.981 r_symmetry_vdw_other 0.255 r_nbd_refined 0.232 r_nbd_other 0.206 r_nbtor_refined 0.193 r_symmetry_hbond_refined 0.191 r_symmetry_vdw_refined 0.189 r_mcbond_other 0.156 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.095 r_nbtor_other 0.095 r_xyhbond_nbd_other 0.091 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 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 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement