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Crystal structure of hydroxyquinol-1,2-dioxygenase from Trametes versicolor (TvHDX1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PACT screen from Molecular Dimensions condition F2 (20 % PEG 3350, 0.2 M sodium bromide, 0.1 M Bis-Tris propane pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.05 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.362 α = 90 b = 54.118 β = 108.385 c = 69.486 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2022-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.459 84.155 94.1 0.058 0.024 0.999 14.2 6.9 87832
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.459 1.572 55 1.143 0.468 0.644 1.4 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.46 84.155 87828 4337 80.806 0.173 0.1717 0.1785 0.2029 0.2097 23.965
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] -0.093 0.152 -0.123 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.567 r_dihedral_angle_3_deg 13.644 r_dihedral_angle_2_deg 12.978 r_dihedral_angle_1_deg 6.211 r_lrange_it 5.945 r_lrange_other 5.835 r_scangle_it 4.162 r_scangle_other 4.161 r_scbond_it 2.795 r_scbond_other 2.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.567 r_dihedral_angle_3_deg 13.644 r_dihedral_angle_2_deg 12.978 r_dihedral_angle_1_deg 6.211 r_lrange_it 5.945 r_lrange_other 5.835 r_scangle_it 4.162 r_scangle_other 4.161 r_scbond_it 2.795 r_scbond_other 2.795 r_mcangle_it 2.596 r_mcangle_other 2.595 r_mcbond_other 1.802 r_mcbond_it 1.801 r_angle_refined_deg 1.587 r_angle_other_deg 0.503 r_symmetry_nbd_refined 0.236 r_nbd_refined 0.222 r_symmetry_xyhbond_nbd_refined 0.187 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.153 r_nbd_other 0.147 r_metal_ion_refined 0.128 r_ncsr_local_group_1 0.108 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4546 Nucleic Acid Atoms Solvent Atoms 566 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing