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Crystal Structure of veratryl alcohol bound Dye Decolorizing peroxidase from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KMM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 26% MPD, 0.05 M HEPES
Crystal Properties Matthews coefficient Solvent content 3.44 64.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.988 α = 87.84 b = 102.108 β = 76.45 c = 105.47 γ = 83.22
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 EIGER R 4M 2018-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.96770 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 45.68 90.6 0.99 7.6 3.38 170472
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 0.82
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6KMM 2.1 45.68 161884 8575 90.63 0.188 0.1848 0.1861 0.2489 0.2485 RANDOM 49.41
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] -1.25 -0.71 -0.9 0.49 -3.58 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.851 r_dihedral_angle_4_deg 20.143 r_dihedral_angle_3_deg 17.019 r_dihedral_angle_1_deg 7.59 r_angle_refined_deg 1.708 r_chiral_restr 0.116 r_gen_planes_refined 0.01 r_bond_refined_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16840 Nucleic Acid Atoms Solvent Atoms 1923 Heterogen Atoms 416
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Coot model building MOLREP phasing