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Crystal Structure of 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 25% MPD, 0.05 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.44 49.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.841 α = 69.59 b = 71.176 β = 83.58 c = 101.014 γ = 80.56
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 2.44 48.15 93.3 0.99 11.2 9.7 52522 55.2
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 2.44 2.48 90.5 0.49 2.1 9.5
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 2.44 48.15 49842 2658 93.25 0.178 0.1746 0.1794 0.2428 0.2427 RANDOM 66.575
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] -0.7 0.65 0.67 0.75 -0.63 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.949 r_dihedral_angle_4_deg 18.456 r_dihedral_angle_3_deg 18.288 r_dihedral_angle_1_deg 7.717 r_angle_refined_deg 1.636 r_chiral_restr 0.121 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11233 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing Coot model building