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Golgi alpha-Mannosidase II in complex with 5-substitued swainsonine analog: (5R)-5-[2'-oxo-2'-(4-methylphenyl)ethyl]-swainsonine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 PEG8000, Tris, pH 7, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.987 α = 90 b = 109.605 β = 90 c = 138.26 γ = 90
Symmetry Space Group P 21 21 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 2004-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9186 CHESS F1
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 1.45 30 99.2 0.0834 14.4 6.24 185662 184195
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 1.45 1.48 95.9 0.369 5.2 5.2 7453
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 (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 3BUB 1.45 29.25 185522 182090 7325 98.15 0.167 0.166 0.1655 0.2 0.163 RANDOM 19.518
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] -0.09 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.568 r_dihedral_angle_4_deg 17.177 r_dihedral_angle_3_deg 12.404 r_dihedral_angle_1_deg 6.076 r_sphericity_free 4.849 r_sphericity_bonded 3.541 r_scangle_it 3.329 r_scbond_it 2.539 r_rigid_bond_restr 1.889 r_mcangle_it 1.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.568 r_dihedral_angle_4_deg 17.177 r_dihedral_angle_3_deg 12.404 r_dihedral_angle_1_deg 6.076 r_sphericity_free 4.849 r_sphericity_bonded 3.541 r_scangle_it 3.329 r_scbond_it 2.539 r_rigid_bond_restr 1.889 r_mcangle_it 1.658 r_angle_refined_deg 1.345 r_mcbond_it 1.15 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.2 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8196 Nucleic Acid Atoms Solvent Atoms 1149 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement CNS refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SADABS data scaling CNS phasing