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Crystal structure of a dye-decolorizing peroxidase R232A variant from Klebsiella pneumoniae (KpDyP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298.15 29% w/v PEG 3350, 0.15 M MgCl2, 0.1 M Tris-HCl, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.25 45.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.16 α = 90 b = 91.16 β = 90 c = 247.82 γ = 120
Symmetry Space Group P 65 2 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 PILATUS3 2M 2017-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.996 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.86 75.23 99.26 0.1134 0.1235 0.04821 0.998 12.11 6.4 51833 27.2494625903
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.927 96.57 1.701 1.847 0.7093 0.589 1.2 6.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6FKS 1.86002782211 75.2221720275 1.32698463845 51706 2566 99.2590033019 0.169650100112 0.167661898902 0.207380987407 0.1805 36.6521148601
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 10.2859720845 f_angle_d 0.731144286828 f_chiral_restr 0.0443890317228 f_bond_d 0.00434800606652 f_plane_restr 0.00341719768381
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4644 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 87
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing