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Crystal structure of the GalNAc-T2 F104S mutant in complex with UDP-GalNAc
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 291 PEG6000, Hepes
Crystal Properties Matthews coefficient Solvent content 2.51 51.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.036 α = 90 b = 154.036 β = 90 c = 109.823 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS3 S 6M 2016-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 154.04 99.7 0.064 0.995 7.8 5.6 70380
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 100 0.72 0.371 1.1 5.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4D0T 2.7 154.04 35697 990 99.61 0.20669 0.20627 0.22104 0.2048 RANDOM 73.516
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] -0.23 -0.23 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.51 r_dihedral_angle_4_deg 19.874 r_dihedral_angle_3_deg 19.698 r_long_range_B_refined 9.12 r_long_range_B_other 9.12 r_dihedral_angle_1_deg 7.3 r_scangle_other 6.199 r_mcangle_it 5.728 r_mcangle_other 5.728 r_scbond_it 3.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.51 r_dihedral_angle_4_deg 19.874 r_dihedral_angle_3_deg 19.698 r_long_range_B_refined 9.12 r_long_range_B_other 9.12 r_dihedral_angle_1_deg 7.3 r_scangle_other 6.199 r_mcangle_it 5.728 r_mcangle_other 5.728 r_scbond_it 3.867 r_scbond_other 3.866 r_mcbond_it 3.516 r_mcbond_other 3.515 r_angle_refined_deg 1.529 r_angle_other_deg 0.968 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 7522 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing