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Crystal structure of dehaloperoxidase B in complex with -(-) limonene oxide
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 277 MPEG 2000, ammonium sulfate, Na cacodylate
Crystal Properties Matthews coefficient Solvent content 2.16 43.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.657 α = 90 b = 66.492 β = 90 c = 68.34 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 2021-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 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 34.193 97.3 0.975 15.3 3.7 31407
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 0.447
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 1.66 34.193 31407 1602 97.314 0.169 0.1659 0.1771 0.2341 0.2386 24.037
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] -1.979 -1.295 3.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.897 r_dihedral_angle_4_deg 19.866 r_dihedral_angle_3_deg 17.554 r_rigid_bond_restr 11.791 r_scangle_it 7.093 r_lrange_it 7.077 r_lrange_other 7.031 r_scangle_other 6.741 r_scbond_it 5.788 r_scbond_other 5.592
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.897 r_dihedral_angle_4_deg 19.866 r_dihedral_angle_3_deg 17.554 r_rigid_bond_restr 11.791 r_scangle_it 7.093 r_lrange_it 7.077 r_lrange_other 7.031 r_scangle_other 6.741 r_scbond_it 5.788 r_scbond_other 5.592 r_dihedral_angle_1_deg 5.364 r_mcangle_other 4.213 r_mcangle_it 4.207 r_mcbond_it 3.499 r_mcbond_other 3.431 r_angle_refined_deg 1.83 r_angle_other_deg 1.568 r_symmetry_nbd_refined 0.298 r_nbd_other 0.275 r_nbd_refined 0.27 r_symmetry_nbd_other 0.229 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.136 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.061 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2132 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing