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Crystal structure of an alcohol-oxidase from Sphingobacterium daejeonense
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A4U9JHU9-F1-model_v4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291.15 10%w/vPEG20000, 20%v/vPEGMME550 0.02Mof each alcohol 0.1MMES/imidazole pH6.5
Crystal Properties Matthews coefficient Solvent content 2.25 45.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.985 α = 90 b = 76.78 β = 98.35 c = 88.222 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 6M 2023-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979180 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 87.29 98.2 0.044 12.4 2.4 71851
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 97.5 0.15 5.3 5.3
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 64.34 68336 3493 97.95 0.16564 0.16351 0.1739 0.20791 0.2152 RANDOM 28.656
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] 2.61 0.24 -1.49 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.174 r_dihedral_angle_1_deg 6.931 r_long_range_B_refined 6.625 r_long_range_B_other 6.566 r_dihedral_angle_2_deg 5.914 r_scangle_other 5.176 r_mcangle_it 3.592 r_mcangle_other 3.592 r_scbond_it 3.421 r_scbond_other 3.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.174 r_dihedral_angle_1_deg 6.931 r_long_range_B_refined 6.625 r_long_range_B_other 6.566 r_dihedral_angle_2_deg 5.914 r_scangle_other 5.176 r_mcangle_it 3.592 r_mcangle_other 3.592 r_scbond_it 3.421 r_scbond_other 3.421 r_mcbond_it 2.629 r_mcbond_other 2.629 r_angle_refined_deg 1.565 r_angle_other_deg 0.545 r_chiral_restr 0.08 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 8394 Nucleic Acid Atoms Solvent Atoms 740 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing