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Crystal structure of dehaloperoxidase B in complex with alpha-terpinene
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 6.5 277.15 MPEG 2000, ammonium sulfate, Na cacodylate
Crystal Properties Matthews coefficient Solvent content 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.716 α = 90 b = 67.532 β = 90 c = 67.44 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 2021-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.718 33.77 99.4 0.056 0.996 31.2 5 30039
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 1.72 1.762 0.803
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 THROUGHOUT 3IXF 1.718 33.766 30039 1466 99.401 0.161 0.1589 0.1554 0.1988 0.1928 28.651
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] 20.295 -5.48 -14.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.814 r_dihedral_angle_4_deg 23.053 r_dihedral_angle_3_deg 18.555 r_lrange_other 8.393 r_lrange_it 8.387 r_dihedral_angle_1_deg 6.909 r_scangle_it 3.519 r_scangle_other 3.514 r_mcangle_other 2.497 r_mcangle_it 2.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.814 r_dihedral_angle_4_deg 23.053 r_dihedral_angle_3_deg 18.555 r_lrange_other 8.393 r_lrange_it 8.387 r_dihedral_angle_1_deg 6.909 r_scangle_it 3.519 r_scangle_other 3.514 r_mcangle_other 2.497 r_mcangle_it 2.496 r_scbond_it 2.441 r_scbond_other 2.44 r_angle_refined_deg 2.169 r_mcbond_other 1.824 r_mcbond_it 1.822 r_angle_other_deg 1.58 r_symmetry_nbd_refined 0.346 r_nbd_refined 0.289 r_symmetry_xyhbond_nbd_refined 0.258 r_symmetry_nbd_other 0.233 r_nbd_other 0.213 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.119 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2151 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing