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Crystal structure of a bacterial fucosidase with inhibitor FucPUG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PEE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Imidazole pH 7.0
0.125 Ammonium Sulfate
16% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.925 α = 90 b = 84.602 β = 109 c = 121.737 γ = 90
Symmetry Space Group I 1 2 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 PILATUS3 6M 2018-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976250 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 1.7 49.61 99.3 0.053 0.03 0.997 11.7 4.2 109676
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 1.7 1.73 98.4 0.347 0.197 0.952 2.7 4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4pee 1.7 49.65 104238 5431 99.14 0.21006 0.20766 0.25393 0.2905 RANDOM 29.593
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] -0.24 -1.53 3.59 -1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.912 r_dihedral_angle_4_deg 16.574 r_dihedral_angle_3_deg 15.687 r_dihedral_angle_1_deg 6.956 r_long_range_B_refined 5.704 r_long_range_B_other 5.635 r_scangle_other 4.017 r_mcangle_it 3.227 r_mcangle_other 3.227 r_scbond_it 2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.912 r_dihedral_angle_4_deg 16.574 r_dihedral_angle_3_deg 15.687 r_dihedral_angle_1_deg 6.956 r_long_range_B_refined 5.704 r_long_range_B_other 5.635 r_scangle_other 4.017 r_mcangle_it 3.227 r_mcangle_other 3.227 r_scbond_it 2.79 r_scbond_other 2.771 r_mcbond_it 2.461 r_mcbond_other 2.46 r_angle_refined_deg 1.6 r_angle_other_deg 1.319 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7153 Nucleic Acid Atoms Solvent Atoms 762 Heterogen Atoms 145
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing