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Structure of P2B11 Glucuronide-3-dehydrogenase
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 0.2 M LiSO4
19% PEG 3350
0.1 M Bis-Tris methane pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.46 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.26 α = 90 b = 185.878 β = 111.2 c = 145.362 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 S 6M 2023-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.18 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.6 48.37 100 0.121 0.13 0.049 0.999 13.7 6.9 161121
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 99.9 1.919 2.074 0.78 0.373 7
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 2.6 48.37 153057 8026 99.96 0.2178 0.21574 0.2201 0.25694 0.2586 RANDOM 71.856
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] 1.22 0.9 -1.5 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.76 r_dihedral_angle_3_deg 18.244 r_long_range_B_other 14.627 r_long_range_B_refined 14.625 r_scangle_other 9.946 r_mcangle_it 9.772 r_mcangle_other 9.772 r_scbond_it 6.656 r_mcbond_it 6.636 r_mcbond_other 6.635
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.76 r_dihedral_angle_3_deg 18.244 r_long_range_B_other 14.627 r_long_range_B_refined 14.625 r_scangle_other 9.946 r_mcangle_it 9.772 r_mcangle_other 9.772 r_scbond_it 6.656 r_mcbond_it 6.636 r_mcbond_other 6.635 r_scbond_other 6.627 r_dihedral_angle_1_deg 5.673 r_angle_refined_deg 1.531 r_angle_other_deg 0.526 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 35839 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 662
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing