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Crystal structure of the L-fucose isomerase from Raoultella sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FUI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 HEPES, PEG10000
Crystal Properties Matthews coefficient Solvent content 2.42 49.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.987 α = 90 b = 127.611 β = 90 c = 257.298 γ = 90
Symmetry Space Group P 21 21 21
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 S 6M 2017-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.9796 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.5 50.01 96.4 0.115 0.13 0.059 7.65 4.1 127420
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 95.4 0.357 0.42 0.216 1.59 3.2
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 1FUI 2.5 50.01 119135 6337 96.34 0.17935 0.17652 0.1832 0.23337 0.2345 RANDOM 35.345
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] -0.37 3.23 -2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.76 r_dihedral_angle_4_deg 21.934 r_dihedral_angle_3_deg 16.236 r_dihedral_angle_1_deg 6.393 r_long_range_B_refined 4.664 r_long_range_B_other 4.651 r_scangle_other 3.093 r_mcangle_it 2.797 r_mcangle_other 2.797 r_scbond_it 2.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.76 r_dihedral_angle_4_deg 21.934 r_dihedral_angle_3_deg 16.236 r_dihedral_angle_1_deg 6.393 r_long_range_B_refined 4.664 r_long_range_B_other 4.651 r_scangle_other 3.093 r_mcangle_it 2.797 r_mcangle_other 2.797 r_scbond_it 2.069 r_scbond_other 2.069 r_mcbond_it 1.738 r_mcbond_other 1.736 r_angle_refined_deg 1.394 r_angle_other_deg 0.807 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 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 27126 Nucleic Acid Atoms Solvent Atoms 1019 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing