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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 4AUL PDB ENTRY 4AUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 PROTEIN CRYSTAL WAS OBTAINED IN 8-18% PEG 4000, 0.2 M POTASSIUM CHLORIDE, 0.01 M CALCIUM CHLORIDE DEHYDRATE AND 0.05 M SODIUM CACODYLATE TRIHYDRATE AT PH 5.0
Crystal Properties Matthews coefficient Solvent content 2.28 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 253.37 α = 90 b = 243.29 β = 104.16 c = 97.06 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 2011-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.9 29.89 99.8 0.13 7.6 3.3 409557 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 1.9 2 100 0.54 2.4 3.3
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 4AUL 1.92 69.94 409557 21640 99.55 0.16605 0.16422 0.1634 0.20054 0.1994 RANDOM 15.535
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] -1.01 -0.95 -0.57 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.154 r_dihedral_angle_4_deg 17.991 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 7.555 r_angle_refined_deg 1.124 r_chiral_restr 0.08 r_gen_planes_refined 0.015 r_bond_refined_d 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.154 r_dihedral_angle_4_deg 17.991 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 7.555 r_angle_refined_deg 1.124 r_chiral_restr 0.08 r_gen_planes_refined 0.015 r_bond_refined_d 0.006 r_bond_other_d r_angle_other_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 41944 Nucleic Acid Atoms Solvent Atoms 3405 Heterogen Atoms 361
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling