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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 2WVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 20% PEG3350, 0.1 M ammonium sulfate, 0.1 M imidazole
Crystal Properties Matthews coefficient Solvent content 2.52 51.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.5 α = 90 b = 188.76 β = 93.89 c = 98.14 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 2.3 67.95 99.7 0.115 0.069 0.992 5.9 3.7 90452
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 2.3 2.34 99.7 1.023 0.616 0.561 1.2 3.7 4527
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 FOURIER SYNTHESIS THROUGHOUT 2WVV 2.3 97.91 85655 4558 99.39 0.2033 0.2012 0.2059 0.2435 0.2472 RANDOM 52.52
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] 4.52 -0.68 -0.07 -4.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.676 r_dihedral_angle_4_deg 19.62 r_dihedral_angle_3_deg 14.653 r_mcangle_it 5.72 r_dihedral_angle_1_deg 5.527 r_mcbond_it 3.882 r_mcbond_other 3.882 r_angle_refined_deg 2.426 r_angle_other_deg 1.555 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.676 r_dihedral_angle_4_deg 19.62 r_dihedral_angle_3_deg 14.653 r_mcangle_it 5.72 r_dihedral_angle_1_deg 5.527 r_mcbond_it 3.882 r_mcbond_other 3.882 r_angle_refined_deg 2.426 r_angle_other_deg 1.555 r_chiral_restr 0.106 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14144 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Aimless data scaling