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Crystal structure of hydroxyquinol-1,2-dioxygenase from Rhodococcus jostii RHA1 (RjTsdC)
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 C10 (20% PEG 6000, 0.2 M magnesium chloride, 0.1 M HEPES pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.12 41.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.61 α = 90 b = 107.411 β = 90 c = 117.814 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 2022-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 1.573 79.375 89.5 0.149 0.042 0.999 12.3 13.1 42534
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 1.573 1.764 76.7 1.581 0.484 0.603 1.7 11.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.573 79.375 42534 2165 53.517 0.185 0.1825 0.1923 0.2279 0.2343 22.895
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] 0.149 -0.01 -0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.771 r_dihedral_angle_3_deg 14.318 r_dihedral_angle_2_deg 11.236 r_lrange_it 6.849 r_lrange_other 6.818 r_dihedral_angle_1_deg 6.812 r_scangle_it 4.478 r_scangle_other 4.478 r_mcangle_it 3.202 r_mcangle_other 3.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.771 r_dihedral_angle_3_deg 14.318 r_dihedral_angle_2_deg 11.236 r_lrange_it 6.849 r_lrange_other 6.818 r_dihedral_angle_1_deg 6.812 r_scangle_it 4.478 r_scangle_other 4.478 r_mcangle_it 3.202 r_mcangle_other 3.202 r_scbond_it 2.791 r_scbond_other 2.791 r_mcbond_other 1.924 r_mcbond_it 1.923 r_angle_refined_deg 1.552 r_angle_other_deg 0.52 r_nbd_other 0.223 r_nbd_refined 0.217 r_symmetry_nbd_refined 0.211 r_xyhbond_nbd_refined 0.194 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.178 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_1 0.084 r_symmetry_xyhbond_nbd_other 0.078 r_chiral_restr 0.07 r_metal_ion_refined 0.058 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 4320 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing