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Crystal structure of human M340H-beta-1,4-galactosyltransferase-1 (M340H-B4GAL-T1) in complex with tetrasaccharide from Lacto-N-neohexose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AEC PDB entry 2AEC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 100 mM mes buffer, 1.6 ammonium sulfate, 2% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.85 68.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.364 α = 90 b = 195.969 β = 90 c = 143.776 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2011-12-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.95 50 93.5 0.04 24.6 3.5 97326 1
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 1.95 2.02 64.2 0.267 3.8 3.1 6991
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 placement THROUGHOUT PDB entry 2AEC 1.95 36.82 93094 5115 93.05 0.1968 0.19498 0.1937 0.23182 0.23 RANDOM 36.777
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.131 r_dihedral_angle_4_deg 16.565 r_dihedral_angle_3_deg 14.027 r_dihedral_angle_1_deg 7.333 r_scangle_it 5.987 r_scbond_it 3.9 r_mcangle_it 2.389 r_angle_refined_deg 1.982 r_mcbond_it 1.499 r_chiral_restr 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.131 r_dihedral_angle_4_deg 16.565 r_dihedral_angle_3_deg 14.027 r_dihedral_angle_1_deg 7.333 r_scangle_it 5.987 r_scbond_it 3.9 r_mcangle_it 2.389 r_angle_refined_deg 1.982 r_mcbond_it 1.499 r_chiral_restr 0.147 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6654 Nucleic Acid Atoms Solvent Atoms 695 Heterogen Atoms 365
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling