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The crystal structure of a Hydroquinone Dioxygenase PaD with nonnatural substrate S6
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 298 0.1 M HEPES 7.0; 24% PEG Smear Medium; 7% Tacsimate 7.0
Crystal Properties Matthews coefficient Solvent content 3.56 65.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.831 α = 90 b = 119.831 β = 90 c = 92.889 γ = 120
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 X 9M 2023-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.9998 NSRRC TPS 05A
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 1.93 25 99.7 0.997 31.6 6 56510
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 1.93 2 0.934
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.93 24.48 53273 2865 98.86 0.21116 0.20905 0.2151 0.24973 0.2545 RANDOM 36.4
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] -0.38 -0.19 -0.38 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.144 r_dihedral_angle_4_deg 18.484 r_dihedral_angle_3_deg 13.822 r_long_range_B_refined 6.369 r_dihedral_angle_1_deg 6.358 r_long_range_B_other 6.336 r_scangle_other 5.207 r_mcangle_it 4.267 r_mcangle_other 4.266 r_scbond_it 3.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.144 r_dihedral_angle_4_deg 18.484 r_dihedral_angle_3_deg 13.822 r_long_range_B_refined 6.369 r_dihedral_angle_1_deg 6.358 r_long_range_B_other 6.336 r_scangle_other 5.207 r_mcangle_it 4.267 r_mcangle_other 4.266 r_scbond_it 3.812 r_scbond_other 3.811 r_mcbond_other 3.633 r_mcbond_it 3.632 r_angle_refined_deg 1.658 r_angle_other_deg 1.426 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3743 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement SAINT data scaling SAINT data reduction PHASER phasing