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Crystal structure of a dye-decolorizing peroxidase D143A 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 298.15 23% w/v PEG 3350, 0.1 M MgCl2, 0.1 M Tris-HCl, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.12 42.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.76 α = 90 b = 76.69 β = 107.79 c = 76.14 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 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 0.966 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 1.27 52.69 97.21 0.03012 0.03792 0.02269 0.999 16.61 1.4 346778 142004 12.7807580788
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 1.27 1.315 96.98 0.4241 0.5324 0.3181 0.794 2.63 2.5
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 1.27000110594 52.6839422655 1.34751905903 141989 6954 97.2141204179 0.115502274903 0.114210014854 0.140849286858 0.1406 18.6598735573
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 14.941459685 f_angle_d 1.07538563247 f_chiral_restr 0.0826241502766 f_bond_d 0.00950616898532 f_plane_restr 0.00747746439931
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4677 Nucleic Acid Atoms Solvent Atoms 795 Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing