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Crystal structure of dehaloperoxidase B in complex with S-(-)-limonene
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, Na cacodylate
Crystal Properties Matthews coefficient Solvent content 2.22 44.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.839 α = 90 b = 67.375 β = 90 c = 67.857 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 1.000 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 37.38 97.91 0.989 26.3 4.7 22814
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 1.918 0.846
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 1.87 37.38 22814 1139 97.906 0.186 0.1846 0.1929 0.2232 0.227 34.874
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] 0.267 0.688 -0.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.069 r_dihedral_angle_4_deg 22.719 r_dihedral_angle_3_deg 17.371 r_lrange_it 7.913 r_lrange_other 7.906 r_dihedral_angle_1_deg 6.23 r_scangle_it 4.195 r_scangle_other 4.165 r_mcangle_other 3.006 r_mcangle_it 3.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.069 r_dihedral_angle_4_deg 22.719 r_dihedral_angle_3_deg 17.371 r_lrange_it 7.913 r_lrange_other 7.906 r_dihedral_angle_1_deg 6.23 r_scangle_it 4.195 r_scangle_other 4.165 r_mcangle_other 3.006 r_mcangle_it 3.005 r_scbond_it 2.905 r_scbond_other 2.875 r_mcbond_it 2.143 r_mcbond_other 2.123 r_angle_refined_deg 1.838 r_angle_other_deg 1.498 r_nbd_refined 0.287 r_symmetry_nbd_other 0.227 r_nbd_other 0.222 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.138 r_symmetry_nbd_refined 0.113 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 r_symmetry_xyhbond_nbd_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2132 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing