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GOLGI MANNOSIDASE II complex with N-octyl-6-epi-valienamine
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 43.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.842 α = 90 b = 109.964 β = 90 c = 138.058 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 BRUKER SMART 6000 2007-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.79 20 98.5 0.061 14.5 4.2 99421 97944
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 1.79 1.83 83.7 0.378 2.6 2 4783
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.79 10.82 99067 97361 1474 98.55 0.156 0.156 0.1597 0.187 RANDOM 16.044
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] 0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.426 r_dihedral_angle_4_deg 18.328 r_dihedral_angle_3_deg 13.595 r_dihedral_angle_1_deg 6.421 r_scangle_it 4.793 r_scbond_it 3.174 r_mcangle_it 2.024 r_angle_refined_deg 1.914 r_mcbond_it 1.253 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.426 r_dihedral_angle_4_deg 18.328 r_dihedral_angle_3_deg 13.595 r_dihedral_angle_1_deg 6.421 r_scangle_it 4.793 r_scbond_it 3.174 r_mcangle_it 2.024 r_angle_refined_deg 1.914 r_mcbond_it 1.253 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.214 r_chiral_restr 0.195 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.161 r_bond_refined_d 0.023 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8192 Nucleic Acid Atoms Solvent Atoms 1170 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement CNS refinement SAINT data scaling PDB_EXTRACT data extraction PROTEUM PLUS data collection SAINT data reduction SADABS data scaling CNS phasing