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Alpha-L-fucosidase AlfC from Lactobacillus casei in complex with alpha-L-fucose product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6O18 PDB entry 6O18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 250 nL 20 mg/mL wild-type AlfC + 250 nL mother liquor (18% w/v PEG3350, 0.1 M Bis-Tris propane, pH 7, 20 mM sodium/potassium phosphate, 1% v/v glycerol), crystals appeared after five days, were harvested in mother liquor + 20% v/v glycerol + 10 mM alpha-L-fucose for ~1 minute, then flash-cooled
Crystal Properties Matthews coefficient Solvent content 2.61 52.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.983 α = 90 b = 138.236 β = 90 c = 264.44 γ = 90
Symmetry Space Group C 2 2 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 EIGER X 16M 2017-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033202 APS 23-ID-B
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 2.6 29.84 99.7 0.056 0.063 0.028 0.998 13.4 4.8 50905
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 2.6 2.68 100 1.292 1.437 0.619 0.484 5.1
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-Factor (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 THROUGHOUT PDB entry 6O18 2.6 29.84 48372 2486 99.45 0.2087 0.2078 0.2168 0.2262 0.2394 RANDOM 101.99
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] -0.85 -1.92 2.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.372 r_dihedral_angle_3_deg 17.214 r_dihedral_angle_4_deg 10.419 r_dihedral_angle_1_deg 6.594 r_angle_refined_deg 1.269 r_angle_other_deg 1.262 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.372 r_dihedral_angle_3_deg 17.214 r_dihedral_angle_4_deg 10.419 r_dihedral_angle_1_deg 6.594 r_angle_refined_deg 1.269 r_angle_other_deg 1.262 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10198 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 44
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction