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Crystal Structure of Human M340H-Beta1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O0R PDB CODE: 1O0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 mes, ammonium sulfate, dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.8 67.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.982 α = 90 b = 195.172 β = 90 c = 143.919 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 ADSC QUANTUM 4 Mirrors 2003-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B 0.97946 NSLS X9B
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 1.98 50 96.5 0.094 15 4.9 101444 1 17.2
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 1.98 2.05 93.1 0.59 2.2 4.2 9651
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB CODE: 1O0R 2 40 97969 97969 9818 96.5 0.233 0.233 0.219 0.2344 0.246 RANDOM 32.2
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] -3.85 13.61 -9.76
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.3 c_scangle_it 3 c_scbond_it 2.09 c_mcangle_it 1.81 c_angle_deg 1.5 c_mcbond_it 1.23 c_improper_angle_d 1.01 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.3 c_scangle_it 3 c_scbond_it 2.09 c_mcangle_it 1.81 c_angle_deg 1.5 c_mcbond_it 1.23 c_improper_angle_d 1.01 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6636 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 306
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing CNS refinement HKL-2000 data reduction