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GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution dataset)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FFV PDB ENTRY 2FFV
Crystallization Crystal Properties Matthews coefficient Solvent content 2.25 45.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.771 α = 90 b = 120.898 β = 90 c = 249.607 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 77 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.85 47 100 0.1 13.5 5.6 83233 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3 100 0.75 2.2 5.6
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 PDB ENTRY 2FFV 2.85 249.61 80867 2285 99.95 0.21655 0.21602 0.219 0.23497 0.2357 RANDOM 75.266
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] 3.78 0.73 -4.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.262 r_dihedral_angle_3_deg 20.693 r_dihedral_angle_4_deg 18.067 r_dihedral_angle_1_deg 6.529 r_mcangle_it 6.47 r_scbond_it 4.264 r_mcbond_it 3.939 r_mcbond_other 3.939 r_angle_other_deg 2.715 r_angle_refined_deg 1.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.262 r_dihedral_angle_3_deg 20.693 r_dihedral_angle_4_deg 18.067 r_dihedral_angle_1_deg 6.529 r_mcangle_it 6.47 r_scbond_it 4.264 r_mcbond_it 3.939 r_mcbond_other 3.939 r_angle_other_deg 2.715 r_angle_refined_deg 1.927 r_chiral_restr 0.105 r_bond_refined_d 0.021 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21608 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 216
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling PHASER phasing