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Crystal structure of bifunctional catalase-phenol oxidase from a marine-derived Cladosporium species complexed with catechol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9HXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 pH 8.5 0.12 M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose;
D-Xylose; N-Acetyl-D-Glucosamine); 0.1 M Imidazole/MES; 30.00% v/v PEG 500 MME; 30.00% v/v PEG 20K
Crystal Properties Matthews coefficient Solvent content 2.55 51.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.868 α = 83 b = 92.08 β = 77.938 c = 168.811 γ = 60.1
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 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 1.95 82.52 90.7 0.132 0.186 0.132 0.99 5 3.8 310143
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 1.95 1.98 1.204 1.702 1.204 0.392 3.9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.95 79.934 309285 15615 90.47 0.258 0.256 0.2606 0.2954 0.2994 37.439
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] -0.634 0.557 0.111 -0.885 -2.008 2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.716 r_dihedral_angle_3_deg 15.346 r_dihedral_angle_2_deg 11.323 r_dihedral_angle_1_deg 7.319 r_lrange_it 6.439 r_lrange_other 6.439 r_scangle_it 4.753 r_scangle_other 4.753 r_mcangle_it 4.38 r_mcangle_other 4.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.716 r_dihedral_angle_3_deg 15.346 r_dihedral_angle_2_deg 11.323 r_dihedral_angle_1_deg 7.319 r_lrange_it 6.439 r_lrange_other 6.439 r_scangle_it 4.753 r_scangle_other 4.753 r_mcangle_it 4.38 r_mcangle_other 4.38 r_scbond_it 3.273 r_scbond_other 3.273 r_mcbond_it 3.11 r_mcbond_other 3.11 r_dihedral_angle_other_2_deg 1.979 r_angle_refined_deg 1.821 r_angle_other_deg 0.638 r_nbd_other 0.351 r_symmetry_xyhbond_nbd_refined 0.327 r_symmetry_nbd_refined 0.32 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.217 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_other 0.113 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.084 r_metal_ion_refined 0.076 r_ncsr_local_group_5 0.062 r_ncsr_local_group_6 0.061 r_ncsr_local_group_12 0.06 r_ncsr_local_group_1 0.059 r_ncsr_local_group_7 0.058 r_ncsr_local_group_27 0.058 r_ncsr_local_group_13 0.057 r_ncsr_local_group_16 0.057 r_ncsr_local_group_17 0.057 r_ncsr_local_group_20 0.057 r_ncsr_local_group_3 0.056 r_ncsr_local_group_4 0.056 r_ncsr_local_group_10 0.056 r_ncsr_local_group_26 0.056 r_ncsr_local_group_15 0.055 r_ncsr_local_group_21 0.055 r_ncsr_local_group_28 0.055 r_ncsr_local_group_9 0.054 r_ncsr_local_group_18 0.054 r_ncsr_local_group_8 0.053 r_ncsr_local_group_25 0.053 r_ncsr_local_group_2 0.052 r_ncsr_local_group_11 0.052 r_ncsr_local_group_22 0.052 r_ncsr_local_group_23 0.051 r_ncsr_local_group_19 0.05 r_ncsr_local_group_24 0.05 r_ncsr_local_group_14 0.046 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32575 Nucleic Acid Atoms Solvent Atoms 2237 Heterogen Atoms 468
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing