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Crystal structure of dehaloperoxidase B in complex with p-cymene
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 2.19 43.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.472 α = 90 b = 66.466 β = 90 c = 68.246 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 2021-09-22 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 1.72 37.2 98.99 0.995 19.8 4.8 29111
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 1.72 1.765 0.751
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 1.72 37.198 29111 1522 98.993 0.18 0.1784 0.1896 0.2107 0.2181 17.746
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] 0.838 -0.367 -0.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.092 r_dihedral_angle_4_deg 24.973 r_dihedral_angle_3_deg 16.776 r_dihedral_angle_1_deg 6.321 r_lrange_it 5.243 r_lrange_other 5.193 r_scangle_it 2.48 r_scangle_other 2.467 r_angle_refined_deg 2 r_mcangle_it 1.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.092 r_dihedral_angle_4_deg 24.973 r_dihedral_angle_3_deg 16.776 r_dihedral_angle_1_deg 6.321 r_lrange_it 5.243 r_lrange_other 5.193 r_scangle_it 2.48 r_scangle_other 2.467 r_angle_refined_deg 2 r_mcangle_it 1.664 r_mcangle_other 1.664 r_angle_other_deg 1.589 r_scbond_it 1.576 r_scbond_other 1.563 r_mcbond_it 1.077 r_mcbond_other 1.077 r_nbd_refined 0.277 r_symmetry_nbd_other 0.228 r_nbd_other 0.215 r_symmetry_xyhbond_nbd_refined 0.192 r_symmetry_nbd_refined 0.187 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2133 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 118
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling REFMAC refinement PHASER phasing