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Crystal structure of hydroxyquinol-1,2-dioxygenase from Gelatoporia subvermispora (GsHDX1)
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 Structure Screen 1+2 from Molecular Dimensions condition F11 (1.6 M ammonium sulfate, 10% 1,4-dioxane, 0.1 M MES pH 6.5)
Crystal Properties Matthews coefficient Solvent content 3.67 66.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.433 α = 90 b = 148.662 β = 90 c = 157.746 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 PIXEL DECTRIS EIGER2 XE 16M 2023-01-29 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 1.777 108.189 94.5 0.175 0.049 0.999 11 13.7 79137
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 1.777 1.971 67.7 1.942 0.526 0.638 1.6 14.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.78 108.189 79136 3939 71.824 0.174 0.1731 0.1971 0.1896 29.612
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] -0.086 -0.064 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.554 r_dihedral_angle_3_deg 14.281 r_dihedral_angle_2_deg 9.915 r_lrange_it 8.222 r_lrange_other 8.143 r_scangle_it 6.129 r_scangle_other 6.022 r_dihedral_angle_1_deg 5.855 r_scbond_it 4.093 r_scbond_other 3.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.554 r_dihedral_angle_3_deg 14.281 r_dihedral_angle_2_deg 9.915 r_lrange_it 8.222 r_lrange_other 8.143 r_scangle_it 6.129 r_scangle_other 6.022 r_dihedral_angle_1_deg 5.855 r_scbond_it 4.093 r_scbond_other 3.999 r_mcangle_it 2.921 r_mcangle_other 2.92 r_mcbond_it 1.983 r_mcbond_other 1.982 r_angle_refined_deg 1.529 r_angle_other_deg 0.497 r_symmetry_xyhbond_nbd_refined 0.23 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.187 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.179 r_symmetry_nbd_refined 0.169 r_nbd_other 0.162 r_symmetry_nbtor_other 0.084 r_metal_ion_refined 0.076 r_chiral_restr 0.071 r_ncsr_local_group_1 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4970 Nucleic Acid Atoms Solvent Atoms 523 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing