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Crystal structure of a bacterial fucosidase with phenyl((1R,2R,3R,4R,5R,6R)-2,3,4-trihydroxy-5-methyl-7-azabicyclo[4.1.0]heptan-7-yl)methanone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 0.1 M imidazole pH 7.0, 0.2 M ammonium sulfate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.65 α = 90 b = 186.52 β = 94.2 c = 98.15 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 PILATUS 6M 2014-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.92 53.2 96.9 0.102 0.058 0.99 7 4 199312
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.95 96.7 0.909 0.539 0.544 1.8 3.7 7178
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 4JFV 1.92 97.89 139018 7350 96.6 0.1849 0.1824 0.1825 0.2318 0.2317 RANDOM 31.583
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] 0.95 -0.75 0.58 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.447 r_dihedral_angle_4_deg 20.794 r_dihedral_angle_3_deg 14.503 r_dihedral_angle_1_deg 6.251 r_mcangle_it 3.834 r_scbond_it 3.637 r_mcbond_it 2.883 r_angle_refined_deg 1.818 r_chiral_restr 0.133 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.447 r_dihedral_angle_4_deg 20.794 r_dihedral_angle_3_deg 14.503 r_dihedral_angle_1_deg 6.251 r_mcangle_it 3.834 r_scbond_it 3.637 r_mcbond_it 2.883 r_angle_refined_deg 1.818 r_chiral_restr 0.133 r_bond_refined_d 0.019 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14236 Nucleic Acid Atoms Solvent Atoms 1204 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction