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Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) (V264G mutant) in complex with UDP-GlcNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LEV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 0.1M bicine pH 9.0 -- 0.05M sodium chloride -- 37.5% PEG300
Crystal Properties Matthews coefficient Solvent content 3.91 68.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.459 α = 90 b = 102.459 β = 90 c = 238.209 γ = 120
Symmetry Space Group P 65 2 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 6M 2016-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.1 59.55 100 0.095 0.101 0.033 0.999 14.4 9.5 14197 85.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.18 100 2.376 2.505 0.784 0.387 1.1 9.9
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 5LEV 3.1 30 13395 728 99.78 0.22327 0.22257 0.2357 0.23624 0.2354 RANDOM 128.475
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] 0.24 0.12 0.24 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.766 r_dihedral_angle_4_deg 16.324 r_dihedral_angle_3_deg 15.474 r_long_range_B_other 9.148 r_long_range_B_refined 9.147 r_scangle_other 5.629 r_mcangle_it 4.669 r_mcangle_other 4.668 r_dihedral_angle_1_deg 3.884 r_scbond_it 3.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.766 r_dihedral_angle_4_deg 16.324 r_dihedral_angle_3_deg 15.474 r_long_range_B_other 9.148 r_long_range_B_refined 9.147 r_scangle_other 5.629 r_mcangle_it 4.669 r_mcangle_other 4.668 r_dihedral_angle_1_deg 3.884 r_scbond_it 3.599 r_scbond_other 3.599 r_mcbond_it 2.968 r_mcbond_other 2.968 r_angle_refined_deg 1.554 r_angle_other_deg 1.018 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 2892 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing