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L-methionine oxidase from Burkholderia bacterium, K304A mutant
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 277 25%(v/v)1,4-Butandiol, 100 mM Tris-HCl (pH 8.0)
Crystal Properties Matthews coefficient Solvent content 4.78 74.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.031 α = 90 b = 122.031 β = 90 c = 295.708 γ = 90
Symmetry Space Group I 41 2 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 PILATUS3 6M 2023-11-27 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) 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 2.1 47.8 99.9 0.999 26.4 26.6 62033
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 0.953
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 2.1 47.79 62033 3248 99.93 0.20941 0.20818 0.217 0.23282 0.2403 RANDOM 57.409
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] 2.71 2.71 -5.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.164 r_dihedral_angle_2_deg 10.045 r_long_range_B_other 9.981 r_long_range_B_refined 9.977 r_scangle_other 8.382 r_dihedral_angle_1_deg 6.918 r_mcangle_other 6.369 r_mcangle_it 6.367 r_scbond_other 6.177 r_scbond_it 6.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.164 r_dihedral_angle_2_deg 10.045 r_long_range_B_other 9.981 r_long_range_B_refined 9.977 r_scangle_other 8.382 r_dihedral_angle_1_deg 6.918 r_mcangle_other 6.369 r_mcangle_it 6.367 r_scbond_other 6.177 r_scbond_it 6.175 r_mcbond_it 5.051 r_mcbond_other 5.032 r_angle_refined_deg 1.97 r_angle_other_deg 0.65 r_chiral_restr 0.086 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 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 3845 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing