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Crystal structure of dehaloperoxidase B in complex with terpinolene
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 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.711 α = 90 b = 67.574 β = 90 c = 67.856 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 2021-07-31 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 1.7 37.383 98.52 0.996 30.3 4.6 30227
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 1.703 1.748 0.547
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 1.703 37.383 30227 1383 98.517 0.188 0.1859 0.1949 0.2247 0.2345 31.851
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] 1.603 -0.669 -0.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.24 r_dihedral_angle_4_deg 22.055 r_dihedral_angle_3_deg 17.54 r_lrange_it 6.964 r_lrange_other 6.904 r_dihedral_angle_1_deg 6.061 r_scangle_it 3.442 r_scangle_other 3.438 r_mcangle_other 2.376 r_mcangle_it 2.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.24 r_dihedral_angle_4_deg 22.055 r_dihedral_angle_3_deg 17.54 r_lrange_it 6.964 r_lrange_other 6.904 r_dihedral_angle_1_deg 6.061 r_scangle_it 3.442 r_scangle_other 3.438 r_mcangle_other 2.376 r_mcangle_it 2.375 r_scbond_it 2.247 r_scbond_other 2.242 r_angle_refined_deg 1.793 r_mcbond_it 1.602 r_mcbond_other 1.602 r_angle_other_deg 1.532 r_nbd_refined 0.284 r_symmetry_nbd_other 0.231 r_nbd_other 0.203 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.167 r_xyhbond_nbd_refined 0.16 r_symmetry_nbd_refined 0.099 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.012 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 111 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing