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Dehaloperoxidase B in complex with 2,2'-Biphenol
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, Sodium Cacodylate
Crystal Properties Matthews coefficient Solvent content 2.21 44.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.239 α = 90 b = 67.702 β = 90 c = 68.038 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 2021-04-18 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 1.93 37.32 99.59 1 13.24 4.5 21108
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 1.93 1.98 0.542
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 FREE R-VALUE 3IXF 1.93 37.318 21108 1005 99.59 0.177 0.174 0.1841 0.2291 0.2329 21.484
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] -0.217 0.487 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.27 r_dihedral_angle_4_deg 21.171 r_dihedral_angle_3_deg 16.816 r_lrange_it 8.788 r_lrange_other 8.773 r_dihedral_angle_1_deg 5.704 r_scangle_it 2.768 r_scangle_other 2.768 r_angle_refined_deg 1.912 r_scbond_it 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.27 r_dihedral_angle_4_deg 21.171 r_dihedral_angle_3_deg 16.816 r_lrange_it 8.788 r_lrange_other 8.773 r_dihedral_angle_1_deg 5.704 r_scangle_it 2.768 r_scangle_other 2.768 r_angle_refined_deg 1.912 r_scbond_it 1.87 r_scbond_other 1.869 r_mcangle_other 1.781 r_mcangle_it 1.78 r_angle_other_deg 1.551 r_mcbond_it 1.145 r_mcbond_other 1.141 r_nbd_refined 0.268 r_symmetry_nbd_refined 0.255 r_nbd_other 0.247 r_symmetry_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.162 r_symmetry_xyhbond_nbd_other 0.16 r_chiral_restr 0.107 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2133 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 199
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing