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Streptococcus pyogenes deacetylase PplD in complex with acetate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 0.2M Zn acetate, 0.1M imidazole pH 8.0, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.21 44.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.16 α = 90 b = 78.43 β = 90 c = 138.07 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 PIXEL DECTRIS PILATUS 6M Rh coated flat bent M0, toroidal focusing post-monochromator M1 2018-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.2700 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.78 39.694 99.3 0.065 0.075 0.999 13.04 3.781 84146 33.462
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.83 97.5 1.126 1.346 0.638 1.09 3.295
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.78 39.694 1.15 84025 4297 99.17 0.1816 0.1797 0.1828 0.2164 0.2153 39.0647
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 9.893 f_angle_d 0.685 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3581 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 61
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing BUCCANEER model building PHENIX refinement PDB_EXTRACT data extraction