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Crystal structure of DyP-type peroxidase from Dictyostelium discoideum in complex with an activated form of oxygen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IIZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 2.4 M sodium malonate pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.35 63.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.03 α = 90 b = 141.03 β = 90 c = 95.56 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.91985 ESRF ID29
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 1.7 47.78 100 0.0314 18.46 26.6 105810 23.43
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 1.7 1.79 100 0.36 2.85 25.44
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2IIZ 1.7 45.25 1.34 105721 5281 99.99 0.1471 0.1461 0.1506 0.1653 0.1701 30.75
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 16.6655 f_angle_d 1.0981 f_chiral_restr 0.0764 f_bond_d 0.0065 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4924 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms 101
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction SADABS data scaling PHASER phasing