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Human ABO(H) blood group glycosyltransferase GTB D302C mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZ7 PDB entry 1LZ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 277 Spontaneous crystals were recovered from concentrated stocks of GTB/D302C (55 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 2.25 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.49 α = 90 b = 150.26 β = 90 c = 78.32 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++ 2005-12-08 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 2.12 19.58 95.3 0.088 0.088 9.1 4.68 17135
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 2.12 2.2 98.8 0.294 3.9 4.56
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 1LZ7 2.12 19.58 16261 874 95.07 0.1953 0.1929 0.2013 0.24 0.2459 RANDOM 35.243
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] -1.8 -1.4 3.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.342 r_dihedral_angle_4_deg 16.808 r_dihedral_angle_3_deg 13.415 r_dihedral_angle_1_deg 6.362 r_mcangle_it 2.218 r_mcbond_it 1.398 r_mcbond_other 1.387 r_angle_refined_deg 1.329 r_angle_other_deg 0.936 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.342 r_dihedral_angle_4_deg 16.808 r_dihedral_angle_3_deg 13.415 r_dihedral_angle_1_deg 6.362 r_mcangle_it 2.218 r_mcbond_it 1.398 r_mcbond_other 1.387 r_angle_refined_deg 1.329 r_angle_other_deg 0.936 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2133 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 6
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction MOLREP phasing