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Golgi mannosidase II D204A catalytic nucleophile mutant complex with METHYL ALPHA-D-MANNOPYRANOSYL-(1->3)-[6-THIO-ALPHA-D-MANNOPYRANOSYL-(1->6)]-BETA-D-MANNOPYRANOSIDE
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 7 293 TRIS, NACL, PEG6000, MPD. Crystals washed in
phosphate buffered reservoir solution before
soaking with substrate for 24 hrs, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.104 α = 90 b = 109.815 β = 90 c = 139.303 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 2005-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.972 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 1.3 20 97.8 0.08 17.2 7.6 260486 254755
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) 1.3 1.32 78.4 0.26 4.8 3.6
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 1.3 19.61 260346 254592 3796 97.79 0.153 0.152 0.1502 0.173 0.1481 RANDOM 16.368
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 36.988 r_dihedral_angle_4_deg 17.691 r_dihedral_angle_3_deg 12.439 r_dihedral_angle_1_deg 6.201 r_sphericity_free 4.005 r_scangle_it 3.45 r_sphericity_bonded 3.401 r_scbond_it 2.43 r_mcangle_it 1.799 r_angle_refined_deg 1.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.988 r_dihedral_angle_4_deg 17.691 r_dihedral_angle_3_deg 12.439 r_dihedral_angle_1_deg 6.201 r_sphericity_free 4.005 r_scangle_it 3.45 r_sphericity_bonded 3.401 r_scbond_it 2.43 r_mcangle_it 1.799 r_angle_refined_deg 1.461 r_rigid_bond_restr 1.447 r_mcbond_it 1.257 r_nbtor_refined 0.309 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_metal_ion_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8581 Nucleic Acid Atoms Solvent Atoms 1706 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing