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Crystal structure of Klebsiella oxytoca ribitol dehydrogenase
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 8.5 293 lithium sulfate, PEG3350, Tris
Crystal Properties Matthews coefficient Solvent content 2.19 43.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.049 α = 90 b = 102.658 β = 109.86 c = 80.984 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 2022-11-25 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 1.97 42.6 99.6 0.092 0.109 0.059 0.994 9 3.4 69343
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 1.97 2.01 99.9 0.608 0.731 0.401 0.695 3.2
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 1.97 42.6 65898 3419 99.58 0.18611 0.18416 0.1921 0.22373 0.227 RANDOM 26.906
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] -0.02 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.431 r_dihedral_angle_4_deg 14.567 r_dihedral_angle_3_deg 14.211 r_dihedral_angle_1_deg 8.187 r_long_range_B_other 5.883 r_long_range_B_refined 5.882 r_scangle_other 4.839 r_mcangle_it 3.682 r_mcangle_other 3.682 r_scbond_it 3.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.431 r_dihedral_angle_4_deg 14.567 r_dihedral_angle_3_deg 14.211 r_dihedral_angle_1_deg 8.187 r_long_range_B_other 5.883 r_long_range_B_refined 5.882 r_scangle_other 4.839 r_mcangle_it 3.682 r_mcangle_other 3.682 r_scbond_it 3.316 r_scbond_other 3.315 r_mcbond_it 2.732 r_mcbond_other 2.732 r_angle_refined_deg 1.378 r_angle_other_deg 1.312 r_chiral_restr 0.065 r_gen_planes_refined 0.011 r_bond_refined_d 0.007 r_gen_planes_other 0.002 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 7296 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PDB_EXTRACT data extraction MOLREP phasing