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Crystal structure of dehaloperoxidase A in complex with substrate 4-nitrocatechol
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 2.18 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.359 α = 90 b = 68.036 β = 90 c = 68.312 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 2023-03-03 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 1.4 44.411 94.65 1 27.5 4.2 51376
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 1.4 1.436 0.873
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 1.4 44.411 51376 2581 94.65 0.168 0.1658 0.172 0.2008 0.2032 15.537
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] -2.185 0.064 2.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.398 r_dihedral_angle_4_deg 20.611 r_dihedral_angle_3_deg 16.673 r_rigid_bond_restr 8.484 r_dihedral_angle_1_deg 5.715 r_lrange_it 3.917 r_lrange_other 3.748 r_scangle_it 3.568 r_scangle_other 3.563 r_scbond_other 3.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.398 r_dihedral_angle_4_deg 20.611 r_dihedral_angle_3_deg 16.673 r_rigid_bond_restr 8.484 r_dihedral_angle_1_deg 5.715 r_lrange_it 3.917 r_lrange_other 3.748 r_scangle_it 3.568 r_scangle_other 3.563 r_scbond_other 3.142 r_scbond_it 3.139 r_mcangle_it 2.668 r_mcangle_other 2.668 r_mcbond_it 2.356 r_mcbond_other 2.353 r_angle_refined_deg 1.998 r_angle_other_deg 1.662 r_nbd_refined 0.317 r_symmetry_nbd_refined 0.273 r_nbd_other 0.271 r_symmetry_xyhbond_nbd_refined 0.248 r_symmetry_nbd_other 0.203 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_other 0.114 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.008 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2183 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing