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Crystal structure of dehaloperoxidase B in complex with gamma-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 MPEG 2000, ammonium sulfate, Na cacodylate
Crystal Properties Matthews coefficient Solvent content 2.22 44.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.817 α = 90 b = 67.606 β = 90 c = 67.62 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) 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 1.7 47.81 99.81 9.1 0.996 10 4.6 30764
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 1.7 1.74 0.768
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 1.7 47.81 30764 1408 99.805 0.201 0.1989 0.2066 0.2453 0.2541 30.962
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] 4.039 -2.575 -1.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.514 r_dihedral_angle_4_deg 20.473 r_dihedral_angle_3_deg 16.685 r_lrange_it 7.886 r_lrange_other 7.883 r_dihedral_angle_1_deg 5.769 r_scangle_it 4.302 r_scangle_other 4.286 r_mcangle_it 3.184 r_mcangle_other 3.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.514 r_dihedral_angle_4_deg 20.473 r_dihedral_angle_3_deg 16.685 r_lrange_it 7.886 r_lrange_other 7.883 r_dihedral_angle_1_deg 5.769 r_scangle_it 4.302 r_scangle_other 4.286 r_mcangle_it 3.184 r_mcangle_other 3.184 r_scbond_it 2.878 r_scbond_other 2.864 r_mcbond_it 2.205 r_mcbond_other 2.205 r_angle_refined_deg 1.555 r_angle_other_deg 1.424 r_nbd_refined 0.261 r_symmetry_nbd_other 0.216 r_symmetry_nbd_refined 0.214 r_nbd_other 0.208 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.145 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2140 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing