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Crystal structure of a dye-decolorizing peroxidase D143AR232A 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 8.5 293.15 29% w/v PEG 3350, 0.15 M MgCl2, 0.1 M Tris-HCl, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.09 41.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.62 α = 90 b = 76.31 β = 107.92 c = 75.94 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 1.09 52.47 98.45 0.04589 0.05555 0.0309 0.998 10.82 2.9 224631 11.1684331273
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 1.09 1.129 98.58 0.691 0.8511 0.4891 0.574 1.28 2.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6FKS 1.09000433235 52.467343562 1.34352684958 224598 11226 98.4556441538 0.125848428175 0.124624616817 0.1249 0.149571192165 0.1497 Random selection 17.1536855966
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 14.6483984313 f_angle_d 1.11310177949 f_chiral_restr 0.0848591615366 f_bond_d 0.00963832472103 f_plane_restr 0.00776087093821
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4665 Nucleic Acid Atoms Solvent Atoms 777 Heterogen Atoms 112
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing