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Golgi alpha-Mannosidase II in complex with Mannostatin analog (1R,2R,3S,4R,5R)-5-aminocyclopentane-1,2,3,4-tetraol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HTY PDB entry 1hty
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 PEG8000, Tris, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7
Crystal Properties Matthews coefficient Solvent content 2.2 44.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.062 α = 90 b = 109.977 β = 90 c = 138.66 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 2007-04-20 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 1.42 40 97.1 0.074 18.2 7.4 193233
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 1.42 1.46 78.8 0.26 6.6 5.1 11985
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 PDB entry 1hty 1.42 19.52 198768 192268 2867 96.73 0.149 0.148 0.1466 0.174 0.145 RANDOM 14.421
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.141 r_dihedral_angle_4_deg 16.963 r_dihedral_angle_3_deg 12.184 r_dihedral_angle_1_deg 6.068 r_sphericity_free 4.78 r_scangle_it 3.998 r_sphericity_bonded 3.078 r_scbond_it 2.743 r_mcangle_it 2.001 r_rigid_bond_restr 1.597
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.141 r_dihedral_angle_4_deg 16.963 r_dihedral_angle_3_deg 12.184 r_dihedral_angle_1_deg 6.068 r_sphericity_free 4.78 r_scangle_it 3.998 r_sphericity_bonded 3.078 r_scbond_it 2.743 r_mcangle_it 2.001 r_rigid_bond_restr 1.597 r_angle_refined_deg 1.47 r_mcbond_it 1.384 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.156 r_xyhbond_nbd_refined 0.131 r_bond_refined_d 0.011 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8187 Nucleic Acid Atoms Solvent Atoms 1399 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SADABS data scaling CNS phasing