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Structure of arginine oxidase from Pseudomonas sp. TRU 7192
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, HANGING DROP 298 20% PEG3350, 0.2M Potassium citrate
Crystal Properties Matthews coefficient Solvent content 2.7 54.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.274 α = 90 b = 200.219 β = 90 c = 168.542 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 S 6M 2018-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.4 49.23 100 0.346 0.144 4.6 6.7 39436
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.47 100 0.977 0.401 2.1
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 3.4 49.04 37466 1970 99.92 0.21698 0.21198 0.2368 0.31298 0.3164 RANDOM 82.559
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] -13.5 3.51 9.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.432 r_dihedral_angle_3_deg 22.65 r_dihedral_angle_4_deg 18.739 r_long_range_B_refined 13.261 r_long_range_B_other 13.261 r_mcangle_it 8.809 r_mcangle_other 8.809 r_scangle_other 8.106 r_dihedral_angle_1_deg 7.35 r_mcbond_it 5.442
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.432 r_dihedral_angle_3_deg 22.65 r_dihedral_angle_4_deg 18.739 r_long_range_B_refined 13.261 r_long_range_B_other 13.261 r_mcangle_it 8.809 r_mcangle_other 8.809 r_scangle_other 8.106 r_dihedral_angle_1_deg 7.35 r_mcbond_it 5.442 r_mcbond_other 5.44 r_scbond_it 4.936 r_scbond_other 4.936 r_angle_refined_deg 1.421 r_angle_other_deg 1.156 r_chiral_restr 0.049 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_gen_planes_other 0.002 r_bond_other_d 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 17447 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing