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Structure of Dehaloperoxidase B in Complex with Thymol
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 2.21 44.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.316 α = 90 b = 66.898 β = 90 c = 67.615 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 1.81 37.344 83.07 0.998 22.1 4.2 20141
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 1.811 1.858 0.793
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 1.96 37.344 16575 838 81.9 0.211 0.2066 0.1986 0.2912 0.287 31.51
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] 19.955 -13.75 -6.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.238 r_dihedral_angle_4_deg 21.65 r_dihedral_angle_3_deg 20.606 r_dihedral_angle_1_deg 7.428 r_lrange_other 6.225 r_lrange_it 6.224 r_scangle_it 2.504 r_scangle_other 2.478 r_mcangle_other 2.384 r_mcangle_it 2.383
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.238 r_dihedral_angle_4_deg 21.65 r_dihedral_angle_3_deg 20.606 r_dihedral_angle_1_deg 7.428 r_lrange_other 6.225 r_lrange_it 6.224 r_scangle_it 2.504 r_scangle_other 2.478 r_mcangle_other 2.384 r_mcangle_it 2.383 r_angle_refined_deg 1.865 r_scbond_it 1.735 r_scbond_other 1.715 r_mcbond_it 1.65 r_mcbond_other 1.649 r_angle_other_deg 1.441 r_symmetry_xyhbond_nbd_other 0.285 r_nbd_refined 0.266 r_symmetry_nbd_other 0.226 r_xyhbond_nbd_refined 0.22 r_symmetry_xyhbond_nbd_refined 0.203 r_nbd_other 0.19 r_nbtor_refined 0.184 r_symmetry_nbd_refined 0.175 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2152 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing