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Crystal structure of an alcohol oxidase from Streptomyces hiroshimensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291.15 30 % Polyethylene glycol 4000
100 mM TRIS pH 8.5
200 mM Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.41 48.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.51 α = 90 b = 97.688 β = 90 c = 68.047 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS 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 97.69 100 0.057 15.4 4.6 36978
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 0.235 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 62.21 35032 1898 99.91 0.15317 0.15102 0.1646 0.19324 0.1993 RANDOM 24.456
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] 0.68 -1.67 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.12 r_dihedral_angle_2_deg 8.949 r_long_range_B_refined 8.338 r_long_range_B_other 7.508 r_dihedral_angle_1_deg 6.689 r_scangle_other 5.18 r_scbond_it 3.455 r_scbond_other 3.455 r_mcangle_other 2.737 r_mcangle_it 2.735
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.12 r_dihedral_angle_2_deg 8.949 r_long_range_B_refined 8.338 r_long_range_B_other 7.508 r_dihedral_angle_1_deg 6.689 r_scangle_other 5.18 r_scbond_it 3.455 r_scbond_other 3.455 r_mcangle_other 2.737 r_mcangle_it 2.735 r_mcbond_it 2.046 r_mcbond_other 2.043 r_angle_refined_deg 1.651 r_angle_other_deg 0.573 r_chiral_restr 0.081 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 3921 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing