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Structure of the blood group glycosyltransferase AAglyB in complex with a pyridine inhibitor as a neutral pyrophosphate surrogate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IOI PDB entry 3IOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 13% or 15% PEG 3350, 50 mM or 150 mM ammonium sulfate and 50 mM MOPS pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.88 α = 90 b = 149.9 β = 90 c = 80.03 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 100 CCD MARMOSAIC 225 mm CCD 2012-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
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 1.7 50 100 0.143 11.44 35437 35437 -3 -3 19.846
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 1.7 1.9 100 0.664 3.02
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3IOI 1.7 42.32 35436 35436 1064 99.98 0.1772 0.1772 0.1763 0.1762 0.205 0.2067 RANDOM 13.989
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] -0.24 0.35 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.166 r_dihedral_angle_4_deg 16.266 r_dihedral_angle_3_deg 11.582 r_dihedral_angle_1_deg 5.558 r_angle_refined_deg 1.064 r_mcangle_it 0.776 r_mcbond_it 0.419 r_scbond_it 0.379 r_chiral_restr 0.078 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.166 r_dihedral_angle_4_deg 16.266 r_dihedral_angle_3_deg 11.582 r_dihedral_angle_1_deg 5.558 r_angle_refined_deg 1.064 r_mcangle_it 0.776 r_mcbond_it 0.419 r_scbond_it 0.379 r_chiral_restr 0.078 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2356 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 58
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction