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Compound II structure of Y389F variant of A type dye-decolourising peroxidase DtpAa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7 293 1:1 v/v solutions of 6.2 mg/ Y389F DtpAa in 20 mM sodium phosphate, 150 mM NaCl pH 7 with a precipitant solution consisting of 100 mM HEPES pH 7, 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.95 36.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.939 α = 90 b = 67.543 β = 104.77 c = 70.797 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 PILATUS 6M-F 2022-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.8 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.01 48.08 99 0.316 0.958 8.9 5.2 45274
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.04 1.174 0.368 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.01 43.88 45241 2186 99.06 0.21003 0.21 0.2083 0.25 0.256 RANDOM 23.522
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] -0.06 -0.48 -0.53 0.74
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.054 f_angle_d 0.765 f_chiral_restr 0.044 f_plane_restr 0.009 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5562 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement DIALS data reduction xia2.multiplex data scaling REFMAC phasing