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Blood group synthase AAGlyB in complex with UDP-GalNAc and cryoprotected with PEG 3350
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZGG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 MOPS buffer, Magnesium sulfate, ammonium sulfate and PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.25 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.635 α = 90 b = 148.386 β = 90 c = 79.816 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 PIXEL DECTRIS PILATUS3 6M 2015-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.072 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.6 42.13 100 0.101 12.4 6.5 41668
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63
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 FOURIER SYNTHESIS FREE R-VALUE 3ZGG 1.6 40 39486 2160 99.91 0.1648 0.16307 0.1757 0.19775 0.2116 RANDOM 15.854
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] -0.99 1.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.118 r_dihedral_angle_4_deg 14.134 r_dihedral_angle_3_deg 12.423 r_dihedral_angle_1_deg 6.356 r_long_range_B_refined 4.112 r_long_range_B_other 3.819 r_scangle_other 2.238 r_angle_refined_deg 1.535 r_mcangle_it 1.487 r_mcangle_other 1.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.118 r_dihedral_angle_4_deg 14.134 r_dihedral_angle_3_deg 12.423 r_dihedral_angle_1_deg 6.356 r_long_range_B_refined 4.112 r_long_range_B_other 3.819 r_scangle_other 2.238 r_angle_refined_deg 1.535 r_mcangle_it 1.487 r_mcangle_other 1.486 r_scbond_it 1.381 r_scbond_other 1.381 r_mcbond_it 0.971 r_mcbond_other 0.959 r_angle_other_deg 0.947 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2343 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing