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Alpha-L-fucosidase AlfC fucosyltransferase mutant N243A
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 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, harvested in mother liquor + 20% v/v glycerol + 5 mM 4-NP-Fuc for ~1 minute, flash-cooled in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.34 47.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.301 α = 90 b = 259.921 β = 118.81 c = 80.35 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2018-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033210 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 47.75 91.5 0.055 0.07 0.042 0.998 8.5 2.3 177005
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 2.03 58.4 0.827 1.074 0.675 0.462 1.8
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 47.75 167908 9045 91.28 0.2307 0.23 0.1803 0.2426 0.1969 RANDOM 48.55
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] -4.9 19.73 -9.95 14.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.868 r_dihedral_angle_3_deg 15.405 r_dihedral_angle_4_deg 8.552 r_dihedral_angle_1_deg 6.942 r_angle_refined_deg 1.46 r_angle_other_deg 1.337 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.868 r_dihedral_angle_3_deg 15.405 r_dihedral_angle_4_deg 8.552 r_dihedral_angle_1_deg 6.942 r_angle_refined_deg 1.46 r_angle_other_deg 1.337 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20791 Nucleic Acid Atoms Solvent Atoms 761 Heterogen Atoms 88
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction