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Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A with galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BYS D_1300016321
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 16 % (w/v) polyethylene glycol (PEG) 10000,
0.1 M ammonium sulfate,
0.1 M bis-tris (pH 5.5),
5 % (v/v) glycerol,
Crystal was soaked into 1 % (w/v) beta-1,3-galactotriose for 5 min
Crystal Properties Matthews coefficient Solvent content 1.98 37.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.818 α = 90 b = 66.565 β = 90 c = 106.39 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 95 CCD ADSC QUANTUM 210 2008-12-07 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 Sym 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 1.5 100 97.5 0.046 48.9 9.2 57278 10.11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 94.9 0.109 21 8.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 D_1300016321 1.5 41.56 57105 2884 97.51 0.1341 0.1344 0.1599 0.1591 Random selection 12.4109
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3218 Nucleic Acid Atoms Solvent Atoms 512 Heterogen Atoms 121
Software Software Software Name Purpose PHENIX refinement REFMAC refinement Coot model building DENZO data reduction SCALEPACK data scaling MOLREP phasing