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Crystal structure of a bacterial fucosidase with iminosugar inhibitor 4-epi-(+)-Codonopsinine
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 7 291.5 0.13 M ammonium sulfate, 12% PEG 6K, 0.1M imidazole pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
Crystal Properties Matthews coefficient Solvent content 3.05 59.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.43 α = 90 b = 95.77 β = 90.81 c = 97.111 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 PILATUS 2M 2012-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91730 Diamond I04-1
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 1.578 97.101 99.2 0.099 9.2 3.9 83920 83920
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 2 2.11 99.6 0.45 0.45 1.7 3.9 12231
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4J27 2 97.1 83920 83899 4187 99.11 0.1584 0.1566 0.1921 0.1911 AS 4J27 25.8593
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] 2.6 -0.82 -0.01 -2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.542 r_dihedral_angle_4_deg 21.993 r_dihedral_angle_3_deg 12.539 r_dihedral_angle_1_deg 5.964 r_mcangle_it 2.563 r_mcbond_it 1.852 r_mcbond_other 1.85 r_angle_refined_deg 1.612 r_angle_other_deg 1.073 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.542 r_dihedral_angle_4_deg 21.993 r_dihedral_angle_3_deg 12.539 r_dihedral_angle_1_deg 5.964 r_mcangle_it 2.563 r_mcbond_it 1.852 r_mcbond_other 1.85 r_angle_refined_deg 1.612 r_angle_other_deg 1.073 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7031 Nucleic Acid Atoms Solvent Atoms 852 Heterogen Atoms 100
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing