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1.75 Angstrom Resolution Crystal Structure of D-alanyl-D-alanine Endopeptidase from Enterobacter cloacae in Complex with Covalently Bound Boronic Acid
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 9.0 mg/mL protein in 0.01 M Tris-HCl, pH 8.3 against screen PACT (B5), 0.1 M MIB buffer, pH 8.0, 25% w/v PEG1500
Crystal Properties Matthews coefficient Solvent content 1.97 37.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.47 α = 90 b = 64.233 β = 90 c = 79.519 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX-300 C(111) 2017-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.75 30 96.8 0.118 0.118 0.058 17.6 4.7 25532 -3 17.6
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) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 100 0.664 0.664 0.334 0.767 2 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.75 29.78 24120 1240 96.69 0.1903 0.18787 0.2 0.23806 0.2462 RANDOM 22.17
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] 3.27 -1.05 -2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.968 r_dihedral_angle_4_deg 12.243 r_dihedral_angle_3_deg 10.854 r_long_range_B_refined 5.418 r_long_range_B_other 5.227 r_scangle_other 3.509 r_dihedral_angle_1_deg 3.288 r_mcangle_it 2.259 r_mcangle_other 2.259 r_scbond_it 2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.968 r_dihedral_angle_4_deg 12.243 r_dihedral_angle_3_deg 10.854 r_long_range_B_refined 5.418 r_long_range_B_other 5.227 r_scangle_other 3.509 r_dihedral_angle_1_deg 3.288 r_mcangle_it 2.259 r_mcangle_other 2.259 r_scbond_it 2.21 r_scbond_other 2.209 r_mcbond_it 1.547 r_mcbond_other 1.536 r_angle_refined_deg 1.338 r_angle_other_deg 0.822 r_chiral_restr 0.054 r_gen_planes_refined 0.024 r_gen_planes_other 0.02 r_bond_refined_d 0.008 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1962 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing