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Structure of Phytolacca americana UGT3 with 15-crown-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M Sodium Bromide
20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.173 α = 90 b = 103.298 β = 90 c = 110.383 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 EIGER X 16M 2018-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 3.1 48.73 99.6 0.16 0.17 0.07 0.99 9.7 6.5 19856
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 3.1 3.31 99 0.72 0.78 0.29 0.8 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2PQ6 3.101 48.726 19805 967 99.498 0.206 0.2027 0.2598 0.2487 65.001
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] -1.757 2.213 -0.455
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.941 r_dihedral_angle_3_deg 19.011 r_dihedral_angle_4_deg 18.531 r_lrange_it 13.341 r_lrange_other 13.341 r_mcangle_other 7.769 r_mcangle_it 7.768 r_scangle_it 7.482 r_scangle_other 7.481 r_dihedral_angle_1_deg 7.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.941 r_dihedral_angle_3_deg 19.011 r_dihedral_angle_4_deg 18.531 r_lrange_it 13.341 r_lrange_other 13.341 r_mcangle_other 7.769 r_mcangle_it 7.768 r_scangle_it 7.482 r_scangle_other 7.481 r_dihedral_angle_1_deg 7.049 r_mcbond_it 4.934 r_mcbond_other 4.926 r_scbond_it 4.576 r_scbond_other 4.576 r_angle_other_deg 2.291 r_angle_refined_deg 1.518 r_metal_ion_refined 0.437 r_symmetry_nbd_other 0.222 r_nbd_refined 0.21 r_nbd_other 0.196 r_symmetry_nbd_refined 0.172 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.126 r_ncsr_local_group_1 0.114 r_chiral_restr 0.072 r_symmetry_nbtor_other 0.069 r_bond_other_d 0.035 r_ext_dist_refined_d 0.021 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7271 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling BALBES phasing