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Expansion of the glycosynthase repertoire to produce defined manno-oligosaccharides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J9Y PDB ENTRY 1J9Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 100MM TRIS 7.5, 26% PEG550, 9MM ZNSO4, 10MM MANNOTETRAOSE, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.855 α = 90 b = 131.855 β = 90 c = 54.268 γ = 90
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 ADSC CCD MIRRORS 2001-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
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 1.4 15 93.7 0.036 29.5 4.01 171242
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 1.4 1.45 64.4 0.384 2.21 2.23
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 1J9Y 1.4 30 162650 8545 93.7 0.152 0.151 0.1619 0.177 0.1879 RANDOM 13.6
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] -0.52 -0.52 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.164 r_scangle_it 2.822 r_scbond_it 1.932 r_mcangle_it 1.401 r_angle_refined_deg 1.4 r_angle_other_deg 1.279 r_mcbond_it 0.952 r_symmetry_vdw_other 0.257 r_nbd_other 0.254 r_nbd_refined 0.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.164 r_scangle_it 2.822 r_scbond_it 1.932 r_mcangle_it 1.401 r_angle_refined_deg 1.4 r_angle_other_deg 1.279 r_mcbond_it 0.952 r_symmetry_vdw_other 0.257 r_nbd_other 0.254 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.126 r_metal_ion_refined 0.124 r_chiral_restr 0.101 r_symmetry_hbond_refined 0.099 r_nbtor_other 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other 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_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6065 Nucleic Acid Atoms Solvent Atoms 1033 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing