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Dehaloperoxidase B in complex with 3,3'-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 2.24 45.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.595 α = 90 b = 67.374 β = 90 c = 67.647 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 PIXEL DECTRIS EIGER X 16M 2021-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
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 1.3 33.85 91.24 0.994 27.88 3.4 62722
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 1.3 1.334 0.645
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 1.3 33.846 62722 3109 91.24 0.148 0.1455 0.145 0.1889 0.1881 16.493
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] -1.641 1.149 0.492
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.46 r_dihedral_angle_3_deg 15.706 r_dihedral_angle_2_deg 9.13 r_rigid_bond_restr 6.3 r_dihedral_angle_1_deg 5.761 r_scangle_other 5.219 r_scangle_it 5.216 r_lrange_it 4.865 r_lrange_other 4.755 r_scbond_other 4.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.46 r_dihedral_angle_3_deg 15.706 r_dihedral_angle_2_deg 9.13 r_rigid_bond_restr 6.3 r_dihedral_angle_1_deg 5.761 r_scangle_other 5.219 r_scangle_it 5.216 r_lrange_it 4.865 r_lrange_other 4.755 r_scbond_other 4.696 r_scbond_it 4.69 r_mcangle_other 3.236 r_mcangle_it 3.235 r_mcbond_it 2.642 r_mcbond_other 2.642 r_angle_refined_deg 1.794 r_angle_other_deg 0.663 r_nbd_refined 0.271 r_nbd_other 0.203 r_nbtor_refined 0.198 r_symmetry_nbd_other 0.188 r_symmetry_xyhbond_nbd_refined 0.181 r_xyhbond_nbd_refined 0.155 r_symmetry_nbd_refined 0.151 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.07 r_symmetry_xyhbond_nbd_other 0.034 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_gen_planes_other 0.009 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2145 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing