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Alpha-L-fucosidase AlfC D200A mutant in complex with 4-nitrophenyl-a-L-fucopyranoside substrate
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 D200Aof + 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 + 5 mM 4NP-Fuc for ~1 minute, flash-cooled in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.61 52.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.734 α = 90 b = 139.079 β = 90 c = 263.373 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 6M 2019-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.033170 SSRL BL12-2
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 39.43 96.7 0.109 0.129 0.068 0.994 6.3 3.4 97990
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 2.64 98.5 1.367 1.621 0.855 0.582 3.3
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 39.43 92904 4998 95.82 0.233 0.2315 0.2374 0.2607 0.2627 RANDOM 70.728
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] -2.38 3.03 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.254 r_dihedral_angle_3_deg 15.609 r_dihedral_angle_4_deg 7.828 r_dihedral_angle_1_deg 6.613 r_angle_refined_deg 1.385 r_angle_other_deg 1.311 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.254 r_dihedral_angle_3_deg 15.609 r_dihedral_angle_4_deg 7.828 r_dihedral_angle_1_deg 6.613 r_angle_refined_deg 1.385 r_angle_other_deg 1.311 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20562 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 160
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction