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Structure of the naturally occuring mutant of human ABO(H) Blood group B glycosyltransferase: GTB/A268T
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 6-8 mg/ml GTB/A268T, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA), pH 7.5, 50 mM CH3COONa, pH 4.6, 40 mM NaCl, 5-8 mM MnCl2, 2.5% (w/v) 2-methyl-2,4-pentanediol (MPD), 5% (w/v) glycerol, 2% (w/v) PEG 4000 and 0.3-0.5 mM
Crystal Properties Matthews coefficient Solvent content 2.3 46.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.54 α = 90 b = 148.95 β = 90 c = 80 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 Osmic "Blue" Confocal x-ray mirrors (Osmic) 2006-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 1.99 20 96.9 0.06 12.9 4.86 21947 21267
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 1.99 2.06 99.4 0.296 4.2 4.6 2128
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 1LZ7 1.99 20 20163 1102 96.85 0.18713 0.1847 0.23063 0.2234 RANDOM 31.973
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] -0.8 0.61 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.768 r_dihedral_angle_4_deg 18.183 r_dihedral_angle_3_deg 14.353 r_dihedral_angle_1_deg 6.642 r_scangle_it 4.085 r_scbond_it 2.774 r_mcangle_it 1.806 r_angle_refined_deg 1.697 r_mcbond_it 1.213 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.768 r_dihedral_angle_4_deg 18.183 r_dihedral_angle_3_deg 14.353 r_dihedral_angle_1_deg 6.642 r_scangle_it 4.085 r_scbond_it 2.774 r_mcangle_it 1.806 r_angle_refined_deg 1.697 r_mcbond_it 1.213 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.126 r_bond_refined_d 0.022 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2143 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling MOLREP phasing