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Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Alanine-D-Alanine and copper (II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MUR pdb entry 4MUR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 0.1 M MgCl2, 0.05 M MES, 20% PEG8K and 0.1 M phenantroline, 2 h incubation, transferred crystal to new drop with 0.1 M MgCl2, 0.05 M MES, 22% PEG8K and 1 mM CuCl2, 1.5 h incubation, transferred crystal to new drop with 0.1 M MgCl2, 0.05 M MES, 22% PEG8K, 1 mM CuCl2 and 20 mM D-Ala-D-Ala. Cryoprotectant: paratone, pH 5.6, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.09 41.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.939 α = 80.53 b = 43.083 β = 74.52 c = 66.316 γ = 64.01
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2013-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 19.33 94.9 0.079 11 3.3 25760 -2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 92.3 0.518 2.3 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 entry 4MUR 2 19.33 1.97 22801 1218 94.81 0.191 0.1886 0.1956 0.2346 0.2369 random
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.776 f_angle_d 0.81 f_chiral_restr 0.045 f_bond_d 0.018 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3150 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 84
Software Software Software Name Purpose CrystalClear data collection PHENIX model building PHENIX refinement XDS data reduction SCALA data scaling PHENIX phasing