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Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Deuteroporphyrin IX and Substrate Trichlorophenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.2 M Ammonium Sulphate
MPEG 2000, 29-33%
Crystal Properties Matthews coefficient Solvent content 2.21 44.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.174 α = 90 b = 67.901 β = 90 c = 67.905 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX300-HS 2019-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM
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 1.98 44.65 98.47 0.997 20.8 4.7 19407
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 1.98 2.03 0.777
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3IXF 1.98 44.65 19407 1040 98.473 0.201 0.1971 0.2051 0.2608 0.2681 30.44
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] 0.948 -0.639 -0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.373 r_dihedral_angle_4_deg 19.921 r_dihedral_angle_3_deg 18.053 r_lrange_it 6.044 r_lrange_other 6.017 r_dihedral_angle_1_deg 5.329 r_scangle_it 3.602 r_scangle_other 3.578 r_mcangle_other 2.609 r_mcangle_it 2.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.373 r_dihedral_angle_4_deg 19.921 r_dihedral_angle_3_deg 18.053 r_lrange_it 6.044 r_lrange_other 6.017 r_dihedral_angle_1_deg 5.329 r_scangle_it 3.602 r_scangle_other 3.578 r_mcangle_other 2.609 r_mcangle_it 2.606 r_scbond_it 2.333 r_angle_refined_deg 2.328 r_scbond_other 2.317 r_mcbond_it 1.665 r_mcbond_other 1.65 r_angle_other_deg 1.554 r_nbd_refined 0.249 r_nbd_other 0.215 r_symmetry_xyhbond_nbd_refined 0.192 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.175 r_symmetry_nbd_refined 0.175 r_chiral_restr 0.141 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.028 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2066 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing