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Crystal structure of bifunctional catalase-phenol oxidase from a marine-derived Cladosporium species
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AUM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M of each amino acid, 0.1 M MES/imidazole pH 6.5
Aminoacids: sodium L-glutamate, 0.2 M DL-alanine, 0.2 M glycine, 0.2 M DL-lysine HCl, 0.2 M DL-serine.
Crystal Properties Matthews coefficient Solvent content 2.67 50.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.549 α = 83.31 b = 92.663 β = 78.177 c = 169.229 γ = 60.329
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 2023-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.6 82.944 91.3 0.061 0.086 0.061 0.995 7 3 577755
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 1.6 1.63 0.729 1.032 0.729 0.549 3.7
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 (All) 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 1.6 82.944 577036 29038 91.452 0.201 0.1994 0.1973 0.2364 0.2342 RANDOM 20.197
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] -0.872 0.206 0.507 0.702 0.097 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.322 r_dihedral_angle_3_deg 13.72 r_dihedral_angle_2_deg 13.086 r_dihedral_angle_1_deg 7.186 r_lrange_it 3.528 r_lrange_other 3.528 r_scangle_it 2.423 r_scangle_other 2.423 r_angle_refined_deg 1.939 r_scbond_it 1.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.322 r_dihedral_angle_3_deg 13.72 r_dihedral_angle_2_deg 13.086 r_dihedral_angle_1_deg 7.186 r_lrange_it 3.528 r_lrange_other 3.528 r_scangle_it 2.423 r_scangle_other 2.423 r_angle_refined_deg 1.939 r_scbond_it 1.649 r_scbond_other 1.649 r_mcangle_it 1.446 r_mcangle_other 1.446 r_mcbond_it 1.047 r_mcbond_other 1.047 r_angle_other_deg 0.706 r_symmetry_nbd_refined 0.316 r_nbd_other 0.255 r_nbd_refined 0.23 r_symmetry_xyhbond_nbd_refined 0.211 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.181 r_symmetry_xyhbond_nbd_other 0.127 r_chiral_restr 0.11 r_symmetry_nbtor_other 0.084 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32589 Nucleic Acid Atoms Solvent Atoms 5122 Heterogen Atoms 725
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing