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Golgi alpha-Mannosidase II in complex with 5-substituted swainsonine analog:(5R)-5-[2'-(4-tert-butylphenyl)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 2.24 45.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.372 α = 90 b = 110.384 β = 90 c = 139.924 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 2005-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.977 CHESS A1
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 1.35 30 99.4 0.0824 14.71 5.96 235192 233665
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 1.35 1.37 97.3 0.258 5.18 4.38 5176
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 1.35 29.55 235037 233580 3468 99.38 0.158 0.158 0.1534 0.176 0.1517 RANDOM 14.852
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] -0.1 0.03 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.055 r_dihedral_angle_4_deg 17.353 r_dihedral_angle_3_deg 11.979 r_dihedral_angle_1_deg 6.017 r_sphericity_free 4.682 r_sphericity_bonded 3.657 r_scangle_it 3.373 r_scbond_it 2.529 r_mcangle_it 1.784 r_rigid_bond_restr 1.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.055 r_dihedral_angle_4_deg 17.353 r_dihedral_angle_3_deg 11.979 r_dihedral_angle_1_deg 6.017 r_sphericity_free 4.682 r_sphericity_bonded 3.657 r_scangle_it 3.373 r_scbond_it 2.529 r_mcangle_it 1.784 r_rigid_bond_restr 1.756 r_angle_refined_deg 1.358 r_mcbond_it 1.281 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.204 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.105 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8193 Nucleic Acid Atoms Solvent Atoms 1284 Heterogen Atoms 50
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