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Exo-alpha-D-arabinofuranosidase from Microbacterium arabinogalactanolyticum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M NaCl, 0.1 M phosphate citrate, 20% PEG8000
Crystal Properties Matthews coefficient Solvent content 3.5 64.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.109 α = 90 b = 207.538 β = 90 c = 253.88 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 PILATUS3 2M 2017-12-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.42 48.24 100 0.147 0.158 0.057 0.995 9.9 7.6 264416 21.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.46 100 0.616 0.661 0.239 0.85 2.8 7.6
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.42 48.24 1.91 264273 13205 99.99 0.1915 0.19 0.198 0.2213 0.2272
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 11.359 f_angle_d 0.939 f_chiral_restr 0.058 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 34813 Nucleic Acid Atoms Solvent Atoms 1027 Heterogen Atoms 60
Software Software Software Name Purpose XDS data reduction Aimless data scaling MoRDa phasing BUCCANEER model building REFMAC refinement PDB_EXTRACT data extraction