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Structure of Phytolacca americana UGT3 with 18-crown-6
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 2.36 47.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.732 α = 90 b = 103.864 β = 90 c = 111.638 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 2018-10-21 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 2.4 49.22 99.8 0.17 0.19 0.07 0.99 11.2 6.6 43272
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 2.4 2.49 99 1.22 1.33 0.52 0.7 6.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2PQ6 2.4 49.217 43210 2119 99.776 0.243 0.2413 0.2475 0.279 0.2812 45.553
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] -0.463 -1.604 2.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.287 r_dihedral_angle_4_deg 18.883 r_dihedral_angle_3_deg 17.791 r_lrange_other 11.275 r_lrange_it 11.272 r_dihedral_angle_1_deg 6.482 r_mcangle_it 6.171 r_mcangle_other 6.171 r_scangle_it 5.862 r_scangle_other 5.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.287 r_dihedral_angle_4_deg 18.883 r_dihedral_angle_3_deg 17.791 r_lrange_other 11.275 r_lrange_it 11.272 r_dihedral_angle_1_deg 6.482 r_mcangle_it 6.171 r_mcangle_other 6.171 r_scangle_it 5.862 r_scangle_other 5.862 r_mcbond_it 3.929 r_mcbond_other 3.918 r_scbond_it 3.605 r_scbond_other 3.605 r_angle_refined_deg 1.522 r_angle_other_deg 1.278 r_metal_ion_refined 0.25 r_nbd_refined 0.202 r_symmetry_nbd_other 0.183 r_symmetry_nbd_refined 0.166 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.163 r_nbd_other 0.156 r_ncsr_local_group_1 0.104 r_symmetry_xyhbond_nbd_refined 0.096 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.029 r_ext_dist_refined_d 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7278 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling BALBES phasing