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Crystal Structure of HEPES bound Dye Decolorizing peroxidase from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GRC
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 3.46 64.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.837 α = 88 b = 101.905 β = 76.43 c = 105.405 γ = 83.28
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 2018-09-28 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 1.93 69.91 92.8 0.99 9.6 6.5 223932
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 1.93 1.96 89.4 0.95 2.2
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 4GRC 1.93 69.91 212663 11128 92.79 0.1626 0.1605 0.1655 0.2018 0.2022 RANDOM 45.601
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] -0.77 -0.81 -0.74 0.62 -2.28 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.944 r_dihedral_angle_4_deg 17.659 r_dihedral_angle_3_deg 16.339 r_dihedral_angle_1_deg 7.371 r_angle_refined_deg 1.789 r_chiral_restr 0.117 r_bond_refined_d 0.011 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16818 Nucleic Acid Atoms Solvent Atoms 2096 Heterogen Atoms 413
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Coot model building MOLREP phasing