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Crystal structure of GalNAc-T4 in complex with the monoglycopeptide 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 PEG3350, ammonium nitrate
Crystal Properties Matthews coefficient Solvent content 2.87 57.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.447 α = 116.47 b = 79.881 β = 96.74 c = 88.614 γ = 104.72
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 2015-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97 Diamond I03
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 1.9 76.45 97.5 0.068 0.988 6.9 3.6 115064
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 95.8 0.556 3.2
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 5AJP 1.9 76.45 111879 3182 97.47 0.22594 0.22459 0.2289 0.27393 0.2804 RANDOM 33.271
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] -0.27 -0.87 -0.62 -0.79 0.53 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.779 r_dihedral_angle_4_deg 16.064 r_dihedral_angle_3_deg 15.744 r_dihedral_angle_1_deg 6.788 r_long_range_B_refined 5.521 r_long_range_B_other 5.521 r_scangle_other 2.328 r_mcangle_other 2.218 r_mcangle_it 2.217 r_angle_refined_deg 1.718
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.779 r_dihedral_angle_4_deg 16.064 r_dihedral_angle_3_deg 15.744 r_dihedral_angle_1_deg 6.788 r_long_range_B_refined 5.521 r_long_range_B_other 5.521 r_scangle_other 2.328 r_mcangle_other 2.218 r_mcangle_it 2.217 r_angle_refined_deg 1.718 r_scbond_it 1.513 r_scbond_other 1.513 r_mcbond_it 1.381 r_mcbond_other 1.379 r_angle_other_deg 1.051 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 8405 Nucleic Acid Atoms Solvent Atoms 1567 Heterogen Atoms 373
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing