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Human ABO(H) blood group glycosyltransferase GTA D302C mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZ0 PDB entry 1LZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 277 Spontaneous crystals were recovered from concentrated stocks of GTA/D302C (95-100 mg/mL) stored in 50 mM MOPS, pH 7.00, 0.1 M sodium chloride, 1 mM DTT, 5 mM manganese chloride, and kept at 277 K.
Crystal Properties Matthews coefficient Solvent content 2.28 46.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.58 α = 90 b = 149.57 β = 90 c = 79.56 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 IMAGE PLATE RIGAKU RAXIS IV++ 2006-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.54 19.79 98.7 0.038 0.038 17.2 4.44 46171
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 1.54 1.6 100 0.32 3.3 3.61
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 PDB entry 1LZ0 1.54 19.79 43837 2329 98.58 0.1824 0.1811 0.2087 0.2204 RANDOM 21.503
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] -0.26 0.6 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.663 r_dihedral_angle_4_deg 16.525 r_dihedral_angle_3_deg 11.867 r_dihedral_angle_1_deg 6.477 r_angle_refined_deg 1.411 r_angle_other_deg 0.958 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.663 r_dihedral_angle_4_deg 16.525 r_dihedral_angle_3_deg 11.867 r_dihedral_angle_1_deg 6.477 r_angle_refined_deg 1.411 r_angle_other_deg 0.958 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2238 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling PDB_EXTRACT data extraction CrystalClear data reduction MOLREP phasing