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Crystal structure of the catalytic domain of the human beta1,4-galactosyltransferase mutant M339H in complex with Mn and UDP-galactose in open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FY7 PDB ENTRY 2FY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 298 10 mg/ml protein solution, 5mM manganese chloride, 5mM UDP-galactose, 50 mM sodium citrate, 6% PEG 4000, pH 5.6, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.56 α = 90 b = 137.73 β = 90 c = 66.43 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 MARRESEARCH mirrors 2002-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 1.85 20 97.1 0.056 22 4.15 27622 1 20
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) 1.85 1.92 92 0.381 3.3 2585
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 2FY7 1.9 19.79 25263 2517 97.6 0.178 0.178 0.1754 0.216 0.211 RANDOM 26.1
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] 2.11 -3.68 1.57
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.9 c_scangle_it 3.05 c_scbond_it 2.13 c_mcangle_it 1.98 c_angle_deg 1.7 c_mcbond_it 1.33 c_improper_angle_d 1.07 c_bond_d 0.014 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.9 c_scangle_it 3.05 c_scbond_it 2.13 c_mcangle_it 1.98 c_angle_deg 1.7 c_mcbond_it 1.33 c_improper_angle_d 1.07 c_bond_d 0.014 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 2194 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 26
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing