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Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Deuteroporphyrin 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 Sulphate
MPEG 2000, 29-33%
Crystal Properties Matthews coefficient Solvent content 2.2 44.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.401 α = 90 b = 67.641 β = 90 c = 67.646 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 2010-06-16 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 1.87 37.28 97.56 0.997 32.7 9.6 22564
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 1.87 1.91 0.997
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 1.87 37.28 21411 1153 97.561 0.206 0.2035 0.2096 0.2502 0.2542 28.394
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] 2.306 -1.04 -1.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.074 r_dihedral_angle_4_deg 22.676 r_dihedral_angle_3_deg 18.456 r_lrange_it 5.493 r_lrange_other 5.458 r_dihedral_angle_1_deg 4.902 r_scangle_it 3.991 r_scangle_other 3.932 r_mcangle_it 2.864 r_mcangle_other 2.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.074 r_dihedral_angle_4_deg 22.676 r_dihedral_angle_3_deg 18.456 r_lrange_it 5.493 r_lrange_other 5.458 r_dihedral_angle_1_deg 4.902 r_scangle_it 3.991 r_scangle_other 3.932 r_mcangle_it 2.864 r_mcangle_other 2.863 r_scbond_it 2.736 r_scbond_other 2.553 r_angle_refined_deg 2.087 r_mcbond_it 2.027 r_mcbond_other 2.023 r_angle_other_deg 1.409 r_symmetry_xyhbond_nbd_refined 0.268 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.231 r_nbd_other 0.224 r_symmetry_nbd_refined 0.2 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.177 r_chiral_restr 0.176 r_symmetry_xyhbond_nbd_other 0.163 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2156 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing