☰ Navigation Tabs
Crystal structure of a bacterial fucosidase with inhibitor 1-phenyl-4-[(2S,3S,4R,5S)-3,4-dihydroxy-5-methylpyrrolidin-2-yl]triazole
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 7 291.15 20% PEG 3350, 0.2 M ammonium sulfate, 0.1 M imidazole
Crystal Properties Matthews coefficient Solvent content 2.48 50.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.04 α = 90 b = 187.59 β = 94.26 c = 97.7 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-F 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) 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 1.95 55.89 98.2 0.081 0.047 8.8 3.9 143082
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 97.4 0.827 0.474 1.7 3.9 7014
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 AB INITIO PHASING THROUGHOUT 4JFV 1.95 97.43 143017 7202 98.06 0.1926 0.1907 0.229 0.2377 RANDOM 37.86
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] 2.28 -1.07 -0.95 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.535 r_dihedral_angle_4_deg 16.583 r_dihedral_angle_3_deg 13.844 r_dihedral_angle_1_deg 5.804 r_mcangle_it 4.384 r_mcbond_it 3.317 r_mcbond_other 3.314 r_angle_refined_deg 1.53 r_angle_other_deg 1.254 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.535 r_dihedral_angle_4_deg 16.583 r_dihedral_angle_3_deg 13.844 r_dihedral_angle_1_deg 5.804 r_mcangle_it 4.384 r_mcbond_it 3.317 r_mcbond_other 3.314 r_angle_refined_deg 1.53 r_angle_other_deg 1.254 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.008 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14284 Nucleic Acid Atoms Solvent Atoms 892 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction