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GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex with Methyl (alpha-D-mannopyranosyl)-(1->3)-S-alpha-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 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.04 α = 90 b = 109.847 β = 90 c = 138.627 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 2006-06-01 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 1.3 20 99.8 0.068 12.9 6.7 256778 256264
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 1.3 1.33 99.6 0.887 2.6 5.5 16843
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 19.84 257039 256139 3801 99.65 0.174 0.174 0.1744 0.192 0.1752 RANDOM 16.953
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 37.004 r_dihedral_angle_4_deg 18.705 r_dihedral_angle_3_deg 12.16 r_dihedral_angle_1_deg 6.087 r_scangle_it 3.539 r_scbond_it 2.32 r_mcangle_it 1.636 r_angle_refined_deg 1.52 r_mcbond_it 1.031 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.004 r_dihedral_angle_4_deg 18.705 r_dihedral_angle_3_deg 12.16 r_dihedral_angle_1_deg 6.087 r_scangle_it 3.539 r_scbond_it 2.32 r_mcangle_it 1.636 r_angle_refined_deg 1.52 r_mcbond_it 1.031 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.101 r_metal_ion_refined 0.019 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8194 Nucleic Acid Atoms Solvent Atoms 1453 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction PDB_EXTRACT data extraction ADSC data collection CNS phasing