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Crystal structure of a dye-decolorizing peroxidase (DyP) from Bacteroides thetaiotaomicron VPI-5482 at 1.6 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 4.5 277 0.2M Li2SO4, 2.5M NaCl, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.98 58.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.09 α = 90 b = 109.09 β = 90 c = 122.1 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2006-03-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97920, 0.97903, 0.91837 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 29.05 99.7 0.097 12.9 14.16 56989 24.466
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 98.7 90.4 0.884 2.3
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 (All) 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 MAD THROUGHOUT 1.6 28.01 56989 2886 99.86 0.165 0.16542 0.164 0.176 0.19 0.197 RANDOM 13.932
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] 0.56 0.28 0.56 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.633 r_dihedral_angle_3_deg 12.043 r_dihedral_angle_4_deg 10.544 r_dihedral_angle_1_deg 5.99 r_scangle_it 4.138 r_scbond_it 2.634 r_mcangle_it 1.017 r_angle_refined_deg 0.957 r_angle_other_deg 0.571 r_mcbond_it 0.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.633 r_dihedral_angle_3_deg 12.043 r_dihedral_angle_4_deg 10.544 r_dihedral_angle_1_deg 5.99 r_scangle_it 4.138 r_scbond_it 2.634 r_mcangle_it 1.017 r_angle_refined_deg 0.957 r_angle_other_deg 0.571 r_mcbond_it 0.408 r_symmetry_vdw_refined 0.273 r_symmetry_vdw_other 0.246 r_nbd_refined 0.22 r_nbd_other 0.202 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_other 0.143 r_symmetry_hbond_refined 0.141 r_nbtor_other 0.089 r_chiral_restr 0.06 r_metal_ion_refined 0.05 r_mcbond_other 0.025 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2388 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SOLVE phasing