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Crystal structure of truncated catechol oxidase from Aspergillus oryzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 294 12% PEG 8000, 10% ethanol, 0.2 M magnesium chloride and 0.1 M
sodium acetate buffer at pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.28 46.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.79 α = 90 b = 95.29 β = 90 c = 139.47 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 210 2010-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9724 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.9 25 93.6 11.4 15.1 14867
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 94.8 0.443 5.6 1428
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 4J3P 2.9 19.87 14122 744 100 0.17875 0.17507 0.1708 0.2481 0.2384 RANDOM 21.374
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] 0.26 0.56 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.726 r_dihedral_angle_4_deg 21.941 r_dihedral_angle_3_deg 16.423 r_dihedral_angle_1_deg 6.035 r_scangle_it 3.553 r_scbond_it 2.12 r_angle_refined_deg 1.401 r_mcangle_it 1.341 r_mcbond_it 0.652 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.726 r_dihedral_angle_4_deg 21.941 r_dihedral_angle_3_deg 16.423 r_dihedral_angle_1_deg 6.035 r_scangle_it 3.553 r_scbond_it 2.12 r_angle_refined_deg 1.401 r_mcangle_it 1.341 r_mcbond_it 0.652 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5296 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 74
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling