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Blood group synthase AAGlyB in its apo form cryoprotected with glycerol
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 7 293 MOPS buffer, Magnesium chloride, ammonium sulfate and PEG3350
Crystal Properties Matthews coefficient Solvent content 2.28 46.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.912 α = 90 b = 149.3 β = 90 c = 80.098 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 2M 2015-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 1.4 42.34 99.6 0.086 11.2 4.9 62538
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 0.748
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 1.4 40 59287 3222 99.51 0.13327 0.13144 0.1297 0.16728 0.1662 RANDOM 16.767
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] 1.21 -0.38 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.864 r_sphericity_free 25.607 r_dihedral_angle_4_deg 19.444 r_sphericity_bonded 14.339 r_dihedral_angle_3_deg 12.032 r_dihedral_angle_1_deg 6.542 r_long_range_B_refined 3.998 r_scbond_it 2.967 r_rigid_bond_restr 2.8 r_mcangle_it 2.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.864 r_sphericity_free 25.607 r_dihedral_angle_4_deg 19.444 r_sphericity_bonded 14.339 r_dihedral_angle_3_deg 12.032 r_dihedral_angle_1_deg 6.542 r_long_range_B_refined 3.998 r_scbond_it 2.967 r_rigid_bond_restr 2.8 r_mcangle_it 2.529 r_mcbond_it 1.911 r_angle_refined_deg 1.643 r_chiral_restr 0.111 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2360 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing