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Crystal structure, recombinant expression and mutagenesis studies of the bifunctional catalase-phenol oxidase from Scytalidium thermophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AUN PDB ENTRY 4AUN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.4 PROTEIN CRYSTAL WAS OBTAINED IN 6-16 % PEG400, 0.2 M POTASSIUM CHLORIDE, 0.01 M CALCIUM CHLORIDE DEHYDRATE AND 0.05 M SODIUM CACODYLATE TRIHYDRATE AT PH 5.4
Crystal Properties Matthews coefficient Solvent content 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.42 α = 90 b = 121.447 β = 115.51 c = 125.208 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315 2011-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.4 29.32 95.3 0.07 16.2 7.1 506416 2
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 1.4 1.48 94.7 0.43 4.4 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 4AUN 1.4 113 481079 25334 95.18 0.11949 0.11812 0.1173 0.1455 0.1449 RANDOM 14.02
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] 0.1 1.06 0.48 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.859 r_sphericity_free 24.474 r_dihedral_angle_4_deg 16.409 r_sphericity_bonded 12.717 r_dihedral_angle_3_deg 11.963 r_dihedral_angle_1_deg 6.034 r_rigid_bond_restr 2.146 r_angle_refined_deg 1.514 r_angle_other_deg 0.391 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.859 r_sphericity_free 24.474 r_dihedral_angle_4_deg 16.409 r_sphericity_bonded 12.717 r_dihedral_angle_3_deg 11.963 r_dihedral_angle_1_deg 6.034 r_rigid_bond_restr 2.146 r_angle_refined_deg 1.514 r_angle_other_deg 0.391 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20973 Nucleic Acid Atoms Solvent Atoms 2463 Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling