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Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F78 pdb entry 4F78
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 273 0.1 M magnesium chloride, 0.05 M MES, 20% PEG 8K, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.19 43.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.239 α = 86.27 b = 44.725 β = 77.7 c = 62.519 γ = 63.74
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 MAR scanner 300 mm plate 2013-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.27696 APS 21-ID-D
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 1.63 40.09 96.8 0.091 18 7.4 50465 -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 1.63 1.83 92.1 0.512 3.4 6.1 13646
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 4F78 1.65 34.449 1.96 46109 2480 95.83 0.1575 0.1553 0.157 0.1993 0.2022 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 15.522 f_angle_d 1.072 f_chiral_restr 0.071 f_bond_d 0.012 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3140 Nucleic Acid Atoms Solvent Atoms 588 Heterogen Atoms 38
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building PHENIX refinement XDS data reduction SCALA data scaling PHENIX phasing