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GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex with Methyl (2-deoxy-2-acetamido-beta-D-glucopyranosyl)-(1->2)-ALPHA-D-mannopyranosyl- (1->3)-[ALPHA-D-mannopyranosyl-(1->6)-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
MOPS 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 2.18 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.744 α = 90 b = 109.457 β = 90 c = 138.358 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 F1 0.918 CHESS F1
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 1.2 20 98.2 0.07 19.1 11.6 324471 318631
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) 1.2 1.24 96.5 0.38 4.2 6.2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB entry 1HTY 1.2 10 323600 313892 4741 97 0.133 0.133 0.17 RANDOM 19.369
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 s_non_zero_chiral_vol 0.092 s_approx_iso_adps 0.091 s_zero_chiral_vol 0.079 s_similar_adp_cmpnt 0.049 s_angle_d 0.032 s_anti_bump_dis_restr 0.03 s_from_restr_planes 0.029 s_bond_d 0.014 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8480 Nucleic Acid Atoms Solvent Atoms 1411 Heterogen Atoms 61
Software Software Software Name Purpose SHELX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SADABS data scaling CNS phasing SHELXL-97 refinement