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Crystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroides thetaiotaomicron in complex with a 5-membered iminocyclitol inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291.15 10.45% PEG 6K, 0.12M ammonium sulfate, 0.095M imidazole, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 3.06 59.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.728 α = 90 b = 95.611 β = 91.21 c = 96.988 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 PSI PILATUS 6M 2011-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.73 29.013 98.3 0.045 12.8 3.2 128218 128218
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.82 94.5 0.449 0.449 1.7 3.2 17914
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 4J27 1.73 29.01 128119 6409 98.13 0.1717 0.1706 0.1801 0.1935 0.2017 RANDOM 34.2843
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] 4.24 -0.86 -0.23 -3.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.448 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 12.653 r_dihedral_angle_1_deg 5.784 r_mcangle_it 3.156 r_mcbond_it 2.434 r_mcbond_other 2.433 r_angle_refined_deg 1.533 r_angle_other_deg 1.047 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.448 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 12.653 r_dihedral_angle_1_deg 5.784 r_mcangle_it 3.156 r_mcbond_it 2.434 r_mcbond_other 2.433 r_angle_refined_deg 1.533 r_angle_other_deg 1.047 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7027 Nucleic Acid Atoms Solvent Atoms 729 Heterogen Atoms 96
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling REFMAC phasing