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Crystal structure of vancomycin resistance D,D-pentapeptidase VanY E175A mutant from VanB-type resistance cassette in complex with Zn(II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MUR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 1.5 M ammonium sulfate, 4% sucrose, 0.01 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.56 51.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.709 α = 101.34 b = 77.319 β = 108.13 c = 85.865 γ = 90.06
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 MARMOSAIC 300 mm CCD 2014-08-08 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) 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 2.3 18.878 98.3 0.084 8.3 3 58200
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 2.3 2.42 97.7 0.412 2.7 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 FREE R-VALUE 4MUR 2.3 18.878 1.96 58200 2941 95.81 0.2219 0.2191 0.221 0.2753 0.2754 Random selection
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 11.883 f_angle_d 0.652 f_chiral_restr 0.033 f_bond_d 0.013 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8669 Nucleic Acid Atoms Solvent Atoms 531 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHENIX phasing PHENIX model building