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crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus in complex with 5-fluoro-alpha-D-xylopyranosyl fluoride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G3M PDB ENTRY 2G3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 25 % PEG MONOMETHYL ETHER 550 (PEG MME 550), 0.1 M BIS-TRIS (PH 7.0)
Crystal Properties Matthews coefficient Solvent content 3.5 64.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.524 α = 90 b = 156.524 β = 90 c = 227.762 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r MIRRORS 2009-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.5 50 99 0.07 10.1 10.1 57181 -3
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 2.5 2.54 99.9 0.75 2 8
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 2G3M 2.503 49.985 1.34 57181 2904 99.76 0.1972 0.1949 0.1936 0.2397 0.238
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] 7.7567 7.7567 -15.5134
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.366 f_angle_d 1.1 f_chiral_restr 0.075 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7572 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement DENZO data reduction SCALEPACK data scaling BALBES phasing