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GalNac-T2 soaked with UDP-sugar
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG
Crystal Properties Matthews coefficient Solvent content 2.45 49.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.575 α = 90 b = 120.126 β = 90 c = 247.389 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 CCD ADSC QUANTUM 315r 2017-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.9753 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.05 39 97.1 0.135 0.09 0.989 7.7 3 64645 44.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.21 98.3 0.771 0.521 0.646 3
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 (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 4d0t 3.05 20.7 61083 3345 96.22 0.23408 0.23123 0.2339 0.28596 0.2854 RANDOM 62.875
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] 5.99 -0.89 -5.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.613 r_dihedral_angle_4_deg 20.179 r_dihedral_angle_3_deg 19.426 r_long_range_B_refined 9.484 r_long_range_B_other 9.483 r_dihedral_angle_1_deg 7.37 r_mcangle_it 6.878 r_mcangle_other 6.878 r_scangle_other 6.108 r_mcbond_it 4.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.613 r_dihedral_angle_4_deg 20.179 r_dihedral_angle_3_deg 19.426 r_long_range_B_refined 9.484 r_long_range_B_other 9.483 r_dihedral_angle_1_deg 7.37 r_mcangle_it 6.878 r_mcangle_other 6.878 r_scangle_other 6.108 r_mcbond_it 4.309 r_mcbond_other 4.309 r_scbond_it 3.831 r_scbond_other 3.831 r_angle_refined_deg 2.06 r_angle_other_deg 1.223 r_chiral_restr 0.138 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.002 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 22685 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing