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Human ABO(H) blood group glycosyltransferase GTB R188K 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 VAPOR DIFFUSION, HANGING DROP 277 GTB/R188K crystals were obtained by hanging drop vapor diffusion at 4 degrees C, where 3 uL of concentrated stock (66-68 mg/mL) was mixed with 1 uL of reservoir solution containing 0.3 M sodium acetate and 0.3 M sodium chloride.
Crystal Properties Matthews coefficient Solvent content 2.28 45.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.67 α = 90 b = 149.67 β = 90 c = 79.18 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++ 2006-10-14 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 1.45 19.81 96.6 0.031 0.031 21 3.84 53903
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 1.45 1.5 96.2 0.283 3.4 3.08
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 1.45 74.74 51167 2733 96.52 0.1897 0.189 0.1891 0.2036 0.2044 RANDOM 20.853
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] -0.71 0.38 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.607 r_dihedral_angle_4_deg 16.484 r_dihedral_angle_3_deg 12.473 r_dihedral_angle_1_deg 6.166 r_angle_refined_deg 1.465 r_angle_other_deg 0.975 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.607 r_dihedral_angle_4_deg 16.484 r_dihedral_angle_3_deg 12.473 r_dihedral_angle_1_deg 6.166 r_angle_refined_deg 1.465 r_angle_other_deg 0.975 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2234 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling PDB_EXTRACT data extraction CrystalClear data reduction MOLREP phasing