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Alditol oxidase from Actinomycetota bacterium in complex with D-xylulose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.12 M Monosaccharides 0.1 M Buffer System 2 7.5 30 % v/v Precipitant Mix 1
Crystal Properties Matthews coefficient Solvent content 2.49 50.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.442 α = 90 b = 109.911 β = 90 c = 296.709 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 EIGER X 16M 2023-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999990 SLS X06SA
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 2.4 49.55 99.8 0.168 0.183 0.071 0.997 7.2 6.7 73369
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 2.4 2.45 99.8 2.581 2.798 1.071 0.587 6.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.4 49.55 69620 3654 99.72 0.24838 0.2463 0.28862 0.2607 RANDOM 67.423
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] 10.06 -2.28 -7.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.438 r_dihedral_angle_4_deg 17.421 r_dihedral_angle_3_deg 15.887 r_long_range_B_refined 10.708 r_long_range_B_other 10.705 r_dihedral_angle_1_deg 7.975 r_mcangle_it 7.869 r_mcangle_other 7.869 r_scangle_other 7.446 r_mcbond_it 5.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.438 r_dihedral_angle_4_deg 17.421 r_dihedral_angle_3_deg 15.887 r_long_range_B_refined 10.708 r_long_range_B_other 10.705 r_dihedral_angle_1_deg 7.975 r_mcangle_it 7.869 r_mcangle_other 7.869 r_scangle_other 7.446 r_mcbond_it 5.189 r_mcbond_other 5.189 r_scbond_it 4.707 r_scbond_other 4.705 r_angle_refined_deg 1.547 r_angle_other_deg 1.18 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 12414 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 252
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing