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Crystal structure of DyP-type peroxidase (SCO2276) from Streptomyces coelicolor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GVK PDB entry 2GVK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 282 Mother liqueur contained 0.2M CaCl2, 0.1M Hepes (pH 7.5) and 28% PEG400. Protein concentration was 15 mg/mL in a buffer containing 100 mM KCl and 50 mM Hepes 8.0. 0.5 uL protein was mixed with equal volume of mother liqueur, VAPOR DIFFUSION, HANGING DROP, temperature 282K
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.99 α = 90 b = 71.99 β = 90 c = 170.81 γ = 120
Symmetry Space Group P 32 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 RAYONIX MX-300 2010-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 30 100 0.095 19.09 9.6 35482 23.97
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 2.05 100 0.675 4.28 4960
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 thorough PDB entry 2GVK 2 29.283 2.02 35482 1774 99.97 0.1613 0.1594 0.1607 0.1975 0.1977 random 24.2439
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.33 f_angle_d 1.01 f_chiral_restr 0.073 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2738 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 46
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection XDS data reduction PHASER phasing