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Crystal Structure of PL-5 family polysaccharide lyase PanPL from Pandoraea apista at pH3.5 in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7FHX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 295.15 0.1 M Citric acid pH 3.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 1.81 32.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.006 α = 90 b = 46.096 β = 91.077 c = 64.586 γ = 90
Symmetry Space Group C 1 2 1
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-F 2018-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.07234 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.099 64.575 89.2 0.076 0.036 0.996 16.7 5.1 15375 14.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.099 2.136 48.9 0.146 0.099 0.975 6.4 2.9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7FHX 2.1 64.57 1.36 15373 799 89.19 0.1915 0.1893 0.1915 0.2297 0.2293 16.21
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 4.012 f_angle_d 0.4874 f_chiral_restr 0.0382 f_plane_restr 0.0032 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2431 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms
Software Software Software Name Purpose Coot model building PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing