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Golgi alpha-Mannosidase II in complex with 5-substituted swainsonine analog:(5S)-5-[2'-oxo-2'-(4-tert-butylphenyl)ethyl]-swainsonine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BUB 3BUBA
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 45.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.372 α = 90 b = 110.543 β = 90 c = 139.985 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 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 1.32 30.07 94.4 0.0775 19.71 8.5 251829 237665
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 1.32 1.35 69.4 0.23 5.3 3.48 10981
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 3BUBA 1.32 30.07 251690 231957 3476 92.16 0.155 0.155 0.154 0.171 0.156 RANDOM 15.467
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] 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.057 r_dihedral_angle_4_deg 18.059 r_dihedral_angle_3_deg 12.162 r_dihedral_angle_1_deg 5.99 r_sphericity_free 4.729 r_sphericity_bonded 3.461 r_scangle_it 3.403 r_scbond_it 2.566 r_rigid_bond_restr 1.806 r_mcangle_it 1.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.057 r_dihedral_angle_4_deg 18.059 r_dihedral_angle_3_deg 12.162 r_dihedral_angle_1_deg 5.99 r_sphericity_free 4.729 r_sphericity_bonded 3.461 r_scangle_it 3.403 r_scbond_it 2.566 r_rigid_bond_restr 1.806 r_mcangle_it 1.784 r_angle_refined_deg 1.344 r_mcbond_it 1.248 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.114 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8197 Nucleic Acid Atoms Solvent Atoms 1112 Heterogen Atoms 48
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