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Golgi alpha-Mannosidase II in complex with Mannostatin analog (1R,2R,3R,4S,5R)-4-amino-5-methoxycyclopentane-1,2,3-triol
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 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.769 α = 90 b = 109.703 β = 90 c = 138.306 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 2007-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9770 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 1.38 40 99.6 0.078 24.2 14.6 212071
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 1.38 1.4 82.8 0.41 5.2 6.7 2887
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 1.38 19.5 212538 211539 3136 99.53 0.188 0.188 0.1822 0.203 0.1833 RANDOM 15.957
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 37.492 r_dihedral_angle_4_deg 17.371 r_dihedral_angle_3_deg 11.731 r_dihedral_angle_1_deg 6.075 r_scangle_it 3.554 r_scbond_it 2.337 r_mcangle_it 1.632 r_angle_refined_deg 1.593 r_mcbond_it 1.07 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.492 r_dihedral_angle_4_deg 17.371 r_dihedral_angle_3_deg 11.731 r_dihedral_angle_1_deg 6.075 r_scangle_it 3.554 r_scbond_it 2.337 r_mcangle_it 1.632 r_angle_refined_deg 1.593 r_mcbond_it 1.07 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.231 r_chiral_restr 0.157 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.137 r_bond_refined_d 0.014 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8197 Nucleic Acid Atoms Solvent Atoms 1304 Heterogen Atoms 34
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