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Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Mesoporphyrin IX and Substrate 4-nitrophenol
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 44.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.138 α = 90 b = 67.927 β = 90 c = 67.867 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 2019-04-04 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 1.56 37.3 94.48 0.998 29.4 3.8 35281
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 1.56 1.6 0.741
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 1.563 37.3 37232 1951 94.483 0.185 0.1836 0.1935 0.2161 0.2224 18.272
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] 0.891 -0.444 -0.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.34 r_dihedral_angle_4_deg 26.497 r_dihedral_angle_3_deg 16.391 r_dihedral_angle_other_2_deg 11.652 r_dihedral_angle_1_deg 5.962 r_lrange_it 3.671 r_lrange_other 3.638 r_scangle_it 2.4 r_scangle_other 2.371 r_angle_refined_deg 2.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.34 r_dihedral_angle_4_deg 26.497 r_dihedral_angle_3_deg 16.391 r_dihedral_angle_other_2_deg 11.652 r_dihedral_angle_1_deg 5.962 r_lrange_it 3.671 r_lrange_other 3.638 r_scangle_it 2.4 r_scangle_other 2.371 r_angle_refined_deg 2.001 r_angle_other_deg 1.636 r_scbond_it 1.584 r_scbond_other 1.561 r_mcangle_it 1.311 r_mcangle_other 1.311 r_mcbond_it 0.872 r_mcbond_other 0.871 r_dihedral_angle_other_1_deg 0.579 r_symmetry_nbd_refined 0.297 r_nbd_other 0.291 r_nbd_refined 0.252 r_nbtor_refined 0.192 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.135 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2159 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing