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Crystal structure of a bacterial fucosidase with iminocyclitol (2S,3S,4R,5S)-3,4-dihydroxy-2-ethynyl-5-methylpyrrolidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MNZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291.15 20% w/v PEG 3350, 0.1 M ammonium sulfate, 0.1 M imidazole
Crystal Properties Matthews coefficient Solvent content 2.79 55.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.08 α = 90 b = 187.699 β = 94.21 c = 97.64 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 PILATUS3 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) 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 2.1 67.57 99.8 0.096 0.992 6.8 3.8 116721
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 99.8 0.891 3.9
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 1MNZ 2.1 67.57 110778 5869 99.75 0.1971 0.1951 0.2011 0.2361 0.24 RANDOM 44.105
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] 2.23 -1.15 0.17 -2.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.431 r_dihedral_angle_4_deg 19.149 r_dihedral_angle_3_deg 14.116 r_dihedral_angle_1_deg 5.793 r_mcangle_it 5.085 r_mcbond_it 3.681 r_mcbond_other 3.679 r_angle_refined_deg 1.505 r_angle_other_deg 1.319 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.431 r_dihedral_angle_4_deg 19.149 r_dihedral_angle_3_deg 14.116 r_dihedral_angle_1_deg 5.793 r_mcangle_it 5.085 r_mcbond_it 3.681 r_mcbond_other 3.679 r_angle_refined_deg 1.505 r_angle_other_deg 1.319 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.008 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14201 Nucleic Acid Atoms Solvent Atoms 773 Heterogen Atoms 140
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing