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Crystal structure of dehaloperoxidase A in complex with substrate 4-nitrophenol
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 2.19 43.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.824 α = 90 b = 67.936 β = 90 c = 68.276 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) 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 2.03 30.43 93.05 0.98 12.4 3.7 16983
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 2.03 2.083 0.314
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 2.03 30.43 16983 841 93.047 0.16 0.1541 0.1637 0.2745 0.2759 28.825
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] -0.758 0.632 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.09 r_dihedral_angle_4_deg 25.425 r_dihedral_angle_3_deg 17.324 r_dihedral_angle_1_deg 6.015 r_lrange_it 5.998 r_lrange_other 5.995 r_scangle_it 5.628 r_scangle_other 5.62 r_mcangle_it 4.785 r_mcangle_other 4.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.09 r_dihedral_angle_4_deg 25.425 r_dihedral_angle_3_deg 17.324 r_dihedral_angle_1_deg 6.015 r_lrange_it 5.998 r_lrange_other 5.995 r_scangle_it 5.628 r_scangle_other 5.62 r_mcangle_it 4.785 r_mcangle_other 4.784 r_scbond_it 4.494 r_scbond_other 4.458 r_mcbond_other 3.826 r_mcbond_it 3.825 r_rigid_bond_restr 2.193 r_angle_refined_deg 1.572 r_angle_other_deg 1.38 r_symmetry_nbd_refined 0.231 r_nbd_refined 0.213 r_symmetry_nbd_other 0.193 r_nbd_other 0.183 r_xyhbond_nbd_refined 0.169 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.131 r_symmetry_xyhbond_nbd_other 0.096 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 103 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing