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Crystal structure of dehaloperoxidase A in complex with substrate 4-bromo-o-cresol
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 MPEG2000, ammonium sulfate, sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.17 43.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.404 α = 90 b = 67.756 β = 90 c = 68.169 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 2022-11-03 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 1.64 37.14 99.79 0.987 30.8 9.3 33787
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 1.64 1.682 0.712
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 1.64 37.136 33787 1678 99.787 0.158 0.1559 0.1689 0.2044 0.2157 19.16
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] 0.435 -0.47 0.035
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.336 r_dihedral_angle_6_deg 15.753 r_dihedral_angle_1_deg 5.358 r_dihedral_angle_2_deg 4.581 r_rigid_bond_restr 3.845 r_lrange_it 2.058 r_lrange_other 2.034 r_angle_refined_deg 1.649 r_scangle_it 1.384 r_scangle_other 1.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.336 r_dihedral_angle_6_deg 15.753 r_dihedral_angle_1_deg 5.358 r_dihedral_angle_2_deg 4.581 r_rigid_bond_restr 3.845 r_lrange_it 2.058 r_lrange_other 2.034 r_angle_refined_deg 1.649 r_scangle_it 1.384 r_scangle_other 1.382 r_mcangle_it 1.196 r_mcangle_other 1.196 r_scbond_it 1.095 r_scbond_other 1.092 r_mcbond_it 0.96 r_mcbond_other 0.958 r_angle_other_deg 0.614 r_nbd_other 0.339 r_nbd_refined 0.325 r_symmetry_nbd_refined 0.325 r_symmetry_nbd_other 0.24 r_symmetry_xyhbond_nbd_refined 0.197 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_other 0.117 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2180 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing