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GOLGI MANNOSIDASE II complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)-2-hydroxy-1 phenylethyl]amino}methyl) pyrrolidin-2-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 PEG 8000, Tris, pH 7, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.923 α = 90 b = 109.993 β = 90 c = 138.909 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 2006-05-31 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 1.2 20 96.1 0.049 12.9 325323 312558
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 1.2 1.25 92.8 0.28 3.68 36427
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 (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R 2F18 1.2 20 313894 280166 3212 95.8 0.109 0.115 0.115 0.1194 0.151 RANDOM 17.701
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_anti_bump_dis_restr 0.179 s_approx_iso_adps 0.101 s_zero_chiral_vol 0.086 s_non_zero_chiral_vol 0.085 s_similar_adp_cmpnt 0.047 s_angle_d 0.03 s_from_restr_planes 0.029 s_bond_d 0.013 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8188 Nucleic Acid Atoms Solvent Atoms 1584 Heterogen Atoms 50
Software Software Software Name Purpose SHELXL-97 refinement SCALEPACK data scaling CNS refinement SHELX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing DENZO data reduction