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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 2.13 42.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.996 α = 90 b = 66.742 β = 90 c = 67.859 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 1.57 36.81 93.5 0.999 22.67 4 35061
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 1.57 1.611 0.66
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 1.57 36.81 35061 1668 93.511 0.147 0.1432 0.143 0.2181 0.2176 26.284
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] -0.626 -2.316 2.942
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.579 r_dihedral_angle_4_deg 20.365 r_dihedral_angle_3_deg 18.507 r_lrange_it 6.644 r_lrange_other 6.59 r_scangle_it 6.379 r_scangle_other 6.33 r_scbond_it 5.658 r_scbond_other 5.474 r_dihedral_angle_1_deg 5.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.579 r_dihedral_angle_4_deg 20.365 r_dihedral_angle_3_deg 18.507 r_lrange_it 6.644 r_lrange_other 6.59 r_scangle_it 6.379 r_scangle_other 6.33 r_scbond_it 5.658 r_scbond_other 5.474 r_dihedral_angle_1_deg 5.312 r_mcangle_other 4.83 r_mcangle_it 4.828 r_rigid_bond_restr 4.788 r_mcbond_it 4.279 r_mcbond_other 4.248 r_angle_refined_deg 1.923 r_angle_other_deg 1.572 r_nbd_refined 0.265 r_nbd_other 0.242 r_symmetry_nbd_refined 0.236 r_symmetry_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.211 r_xyhbond_nbd_refined 0.201 r_nbtor_refined 0.184 r_chiral_restr 0.115 r_symmetry_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.084 r_xyhbond_nbd_other 0.02 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2135 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing