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Dye-decolorizing peroxidase (DyP) complex with ascorbic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 278 PEG8000, pH 6.0, vapor diffusion, hanging drop, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.31 46.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.892 α = 90 b = 95.912 β = 103.81 c = 50.333 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210 2012-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
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 1.5 50 99.5 0.05 12.7 3.8 68745
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 1.5 1.53 98.9 0.283 3.7 3422
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 3AFV 1.5 48.88 68666 3483 99.34 0.1738 0.1727 0.1774 0.1926 0.1973 RANDOM 11.251
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] 1.38 0.33 -0.87 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.455 r_dihedral_angle_4_deg 21.252 r_dihedral_angle_3_deg 10.802 r_dihedral_angle_1_deg 5.779 r_angle_refined_deg 1.235 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3331 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 55
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction