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Phenylethanol rhamnosyltransferase (CmGT3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other AF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 Precipitation Reagent: 20% (w/v) PEG 8000, Buffer: 100 mM CHES/ Sodium hydroxide pH 9.5
Crystal Properties Matthews coefficient Solvent content 4.27 71.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.574 α = 90 b = 183.574 β = 90 c = 90.2 γ = 120
Symmetry Space Group P 31 2 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 EIGER2 S 9M 2023-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 2.62 158.98 99.4 0.998 17.2 19.2 52356
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 2.62 2.69 0.698
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 2.62 158.98 49668 2659 99.22 0.21203 0.21016 0.2158 0.2478 0.2511 RANDOM 61.645
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] 0.95 0.48 0.95 -3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.624 r_dihedral_angle_4_deg 20.127 r_dihedral_angle_3_deg 16.735 r_long_range_B_refined 9.765 r_long_range_B_other 9.765 r_scangle_other 7.246 r_mcangle_it 6.765 r_mcangle_other 6.764 r_dihedral_angle_1_deg 6.068 r_scbond_it 4.639
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.624 r_dihedral_angle_4_deg 20.127 r_dihedral_angle_3_deg 16.735 r_long_range_B_refined 9.765 r_long_range_B_other 9.765 r_scangle_other 7.246 r_mcangle_it 6.765 r_mcangle_other 6.764 r_dihedral_angle_1_deg 6.068 r_scbond_it 4.639 r_scbond_other 4.635 r_mcbond_it 4.484 r_mcbond_other 4.484 r_angle_refined_deg 1.485 r_angle_other_deg 0.831 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 7040 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DIALS data scaling Adxv data reduction PHENIX model building