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Crystal structure of a bacterial fucosidase with a multivalent iminocyclitol inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J27 PDB ENTRY 4J27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291.5 85% dilution of (0.13M AS, 15% PEG6K, 0.1M imidazole pH 7), VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
Crystal Properties Matthews coefficient Solvent content 3.06 59.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.378 α = 90 b = 96.047 β = 91.29 c = 97.204 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 PSI PILATUS 6M 2011-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.68 48.707 99 0.095 6.6 3.2 141254 141254
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.77 99.6 0.501 0.501 1.5 3.1 20667
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 4J27 1.68 48.707 141254 141053 7027 98.79 0.1662 0.1649 0.1754 0.1917 0.201 AS PDB ENTRY 4J27 25.4304
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] 2.37 -0.46 -0.67 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.992 r_dihedral_angle_4_deg 20.112 r_dihedral_angle_3_deg 11.97 r_dihedral_angle_1_deg 6.142 r_mcangle_it 2.725 r_mcbond_it 1.978 r_mcbond_other 1.977 r_angle_refined_deg 1.705 r_angle_other_deg 1.291 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.992 r_dihedral_angle_4_deg 20.112 r_dihedral_angle_3_deg 11.97 r_dihedral_angle_1_deg 6.142 r_mcangle_it 2.725 r_mcbond_it 1.978 r_mcbond_other 1.977 r_angle_refined_deg 1.705 r_angle_other_deg 1.291 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7048 Nucleic Acid Atoms Solvent Atoms 1055 Heterogen Atoms 107
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction REFMAC phasing