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Crystal structure of the fucosylgalactoside alpha N- acetylgalactosaminyltransferase (GTA P156L mutant) in complex with UDP and deoxy-H-antigen acceptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y7A PDB ENTRY 2Y7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 5 MM MOPS PH 7.0, 1 MM MNCL2, 1 MM DTT, 0.1 M AMSO4, 10% (W/V) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.51 α = 90 b = 52.61 β = 89.97 c = 80.27 γ = 90
Symmetry Space Group C 1 2 1
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 MARRESEARCH 165 2008-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 MAX II I911-2
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 2.46 54.5 96.8 0.13 11.6 3.6 21693 25.7
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 2.46 2.59 78 0.32 3.2 3.1
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 2Y7A 2.48 36.88 20949 1120 99.48 0.14693 0.14503 0.1338 0.18203 0.1592 RANDOM 12.51
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] 0.13 0.31 -0.38 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.209 r_dihedral_angle_4_deg 15.983 r_dihedral_angle_3_deg 14.835 r_dihedral_angle_1_deg 6.115 r_angle_refined_deg 1.376 r_mcangle_it 1.202 r_angle_other_deg 0.876 r_scbond_it 0.847 r_mcbond_it 0.799 r_mcbond_other 0.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.209 r_dihedral_angle_4_deg 15.983 r_dihedral_angle_3_deg 14.835 r_dihedral_angle_1_deg 6.115 r_angle_refined_deg 1.376 r_mcangle_it 1.202 r_angle_other_deg 0.876 r_scbond_it 0.847 r_mcbond_it 0.799 r_mcbond_other 0.799 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4726 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing