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Crystal structure of dehaloperoxidase B in complex with 2,6-dichlorophenol
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 MPEG 2000, ammonium sulfate, sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.18 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.84 α = 90 b = 67.31 β = 90 c = 68.03 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 PIXEL DECTRIS EIGER X 16M 2021-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 1.66 37.15 84.58 0.998 11.2 3.3 27584
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 1.66 1.703 0.821
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 1.66 37.15 27584 1329 84.582 0.189 0.1863 0.1976 0.2411 0.2427 24.041
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] 1.1 -0.441 -0.659
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.417 r_dihedral_angle_4_deg 20.101 r_dihedral_angle_3_deg 17.216 r_lrange_other 8.288 r_lrange_it 8.286 r_dihedral_angle_1_deg 6.06 r_scangle_it 3.253 r_scangle_other 3.239 r_mcangle_other 2.188 r_mcangle_it 2.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.417 r_dihedral_angle_4_deg 20.101 r_dihedral_angle_3_deg 17.216 r_lrange_other 8.288 r_lrange_it 8.286 r_dihedral_angle_1_deg 6.06 r_scangle_it 3.253 r_scangle_other 3.239 r_mcangle_other 2.188 r_mcangle_it 2.186 r_scbond_it 2.145 r_scbond_other 2.056 r_angle_refined_deg 1.979 r_angle_other_deg 1.585 r_mcbond_it 1.436 r_mcbond_other 1.428 r_nbd_refined 0.268 r_symmetry_nbd_other 0.197 r_nbd_other 0.195 r_nbtor_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.17 r_xyhbond_nbd_refined 0.169 r_symmetry_nbd_refined 0.15 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.047 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2132 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing