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Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Mesoporphyrin IX and Substrate 4-bromophenol
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 Sulfate,
MPEG 2000, 29-33%
Crystal Properties Matthews coefficient Solvent content 2.24 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.656 α = 90 b = 67.432 β = 90 c = 67.547 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 2019-06-16 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 1.67 33.77 94.53 0.997 28.6 4.4 31197
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 1.67 1.71 0.746
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 1.67 33.77 31197 1546 94.531 0.169 0.1683 0.1629 0.1884 0.1861 17.85
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] 6.225 -2.455 -3.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.578 r_dihedral_angle_4_deg 21.195 r_dihedral_angle_3_deg 18.391 r_dihedral_angle_other_2_deg 15.509 r_dihedral_angle_other_1_deg 12.796 r_dihedral_angle_1_deg 5.478 r_lrange_it 3.077 r_lrange_other 3.036 r_angle_refined_deg 1.73 r_angle_other_deg 1.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.578 r_dihedral_angle_4_deg 21.195 r_dihedral_angle_3_deg 18.391 r_dihedral_angle_other_2_deg 15.509 r_dihedral_angle_other_1_deg 12.796 r_dihedral_angle_1_deg 5.478 r_lrange_it 3.077 r_lrange_other 3.036 r_angle_refined_deg 1.73 r_angle_other_deg 1.457 r_scangle_it 1.253 r_scangle_other 1.234 r_mcangle_it 0.866 r_mcangle_other 0.866 r_scbond_it 0.816 r_scbond_other 0.804 r_mcbond_it 0.544 r_mcbond_other 0.542 r_nbd_refined 0.246 r_symmetry_nbd_refined 0.229 r_nbd_other 0.22 r_xyhbond_nbd_refined 0.19 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.143 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.048 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2155 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing