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Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with D-allulose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JO9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 ammonium sulfate, isopropanol, PEG8000, HEPES
Crystal Properties Matthews coefficient Solvent content 2.19 43.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.008 α = 90 b = 102.869 β = 109.7 c = 80.574 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 S 6M 2023-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.56 42.61 99.5 0.034 0.041 0.022 1 20.1 3.3 138604
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.59 99.3 0.512 0.625 0.354 0.77 2.9
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 1.56 42.61 131793 6779 99.46 0.16982 0.16867 0.1791 0.19226 0.2001 RANDOM 22.743
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.939 r_dihedral_angle_4_deg 15.203 r_dihedral_angle_3_deg 14.203 r_dihedral_angle_1_deg 8.262 r_long_range_B_other 7.13 r_long_range_B_refined 7.122 r_scangle_other 6.053 r_scbond_it 4.467 r_scbond_other 4.466 r_mcangle_it 4.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.939 r_dihedral_angle_4_deg 15.203 r_dihedral_angle_3_deg 14.203 r_dihedral_angle_1_deg 8.262 r_long_range_B_other 7.13 r_long_range_B_refined 7.122 r_scangle_other 6.053 r_scbond_it 4.467 r_scbond_other 4.466 r_mcangle_it 4.141 r_mcangle_other 4.141 r_mcbond_it 3.222 r_mcbond_other 3.222 r_angle_other_deg 1.358 r_angle_refined_deg 1.219 r_chiral_restr 0.06 r_gen_planes_refined 0.009 r_bond_refined_d 0.006 r_gen_planes_other 0.001 r_bond_other_d 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 7405 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PDB_EXTRACT data extraction MOLREP phasing