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Crystal structure of alpha-L-fucosidase from Vibrio sp. strain EJY3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Sodium dihydrogen phosphate, Potassium hydrogen phosphate, acetate
Crystal Properties Matthews coefficient Solvent content 3.17 61.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.916 α = 90 b = 163.916 β = 90 c = 58.712 γ = 120
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 270 2017-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 50 95.3 0.075 0.081 0.029 12.8 7.6 67820
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 1.9 1.93 96.8 0.328 0.352 0.126 0.952 7.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.9 28.5 64319 3393 95.07 0.1723 0.1707 0.1823 0.2033 0.2096 RANDOM 23.593
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] 0.12 0.06 0.12 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.798 r_dihedral_angle_4_deg 15.523 r_dihedral_angle_3_deg 13.321 r_dihedral_angle_1_deg 7.179 r_angle_refined_deg 1.837 r_angle_other_deg 1.474 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.798 r_dihedral_angle_4_deg 15.523 r_dihedral_angle_3_deg 13.321 r_dihedral_angle_1_deg 7.179 r_angle_refined_deg 1.837 r_angle_other_deg 1.474 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4793 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing