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Crystal structure of Dehaloperoxidase A in complex with substrate 2,4-dibromophenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 MPEG 2000, ammonium sulfate, sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.1 41.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.171 α = 90 b = 66.182 β = 90 c = 69.063 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 2022-09-25 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) Rpim I (All) 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 1.515 36.691 99.62 0.086 0.979 21 8.8 41266
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 1.52 1.554 0.582
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 PDB entry 2QFK 1.515 36.691 41266 2050 99.616 0.182 0.1808 0.1905 0.2052 0.2095 16.331
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] 0.617 -0.408 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.364 r_dihedral_angle_4_deg 24.064 r_dihedral_angle_3_deg 16.973 r_dihedral_angle_1_deg 5.89 r_lrange_it 5.269 r_lrange_other 5.228 r_scangle_other 3.892 r_scangle_it 3.89 r_scbond_it 2.583 r_scbond_other 2.575
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.364 r_dihedral_angle_4_deg 24.064 r_dihedral_angle_3_deg 16.973 r_dihedral_angle_1_deg 5.89 r_lrange_it 5.269 r_lrange_other 5.228 r_scangle_other 3.892 r_scangle_it 3.89 r_scbond_it 2.583 r_scbond_other 2.575 r_mcangle_it 2.012 r_mcangle_other 2.011 r_angle_refined_deg 1.764 r_angle_other_deg 1.578 r_mcbond_it 1.312 r_mcbond_other 1.306 r_symmetry_nbd_refined 0.315 r_nbd_refined 0.265 r_nbd_other 0.263 r_symmetry_xyhbond_nbd_refined 0.211 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.176 r_xyhbond_nbd_other 0.105 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.012 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 2182 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement Epinorm data reduction SCALEPACK data scaling PHASER phasing