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Crystal structure of Tagatose 4-epimerase with one glycerol from Thermoprotei archaeon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A662GG58-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M HEPES pH 7.5
42% v/v Polyethylene glycol 200
5 mM Nickel sulfate
Crystal Properties Matthews coefficient Solvent content 2.61 52.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.42 α = 90 b = 76.23 β = 100.64 c = 90.93 γ = 90
Symmetry Space Group C 1 2 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 Bruker PHOTON II multilayer 2024-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.13 45.64 95.9 0.997 11.3 2 31435
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.19 0.729
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.13 45.64 29911 1519 95.58 0.17752 0.17553 0.1882 0.21717 0.226 RANDOM 33.468
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] 1.45 -1.53 0.28 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.999 r_dihedral_angle_4_deg 15.902 r_dihedral_angle_3_deg 14.599 r_dihedral_angle_1_deg 5.966 r_long_range_B_refined 5.766 r_long_range_B_other 5.698 r_scangle_other 4.142 r_mcangle_it 2.934 r_mcangle_other 2.933 r_scbond_it 2.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.999 r_dihedral_angle_4_deg 15.902 r_dihedral_angle_3_deg 14.599 r_dihedral_angle_1_deg 5.966 r_long_range_B_refined 5.766 r_long_range_B_other 5.698 r_scangle_other 4.142 r_mcangle_it 2.934 r_mcangle_other 2.933 r_scbond_it 2.565 r_scbond_other 2.565 r_mcbond_it 1.908 r_mcbond_other 1.903 r_angle_refined_deg 1.362 r_angle_other_deg 0.767 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 3943 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing