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Golgi alpha-Mannosidase II in complex with Mannostatin analog (1S,2S,3R,4R)-4-aminocyclopentane-1,2,3-triol
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 7 298 PEG8000, Tris, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7
Crystal Properties Matthews coefficient Solvent content 2.19 43.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.917 α = 90 b = 109.539 β = 90 c = 138.689 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 1.21 20 96.2 0.066 14.1 6.9 305324
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 1.21 1.24 87.9 0.54 3.4 4 18434
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB entry 1HTY 1.21 20 300722 258803 4530 94.7 0.127 0.127 0.1236 0.163 RANDOM 20.368
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 s_approx_iso_adps 0.101 s_non_zero_chiral_vol 0.091 s_zero_chiral_vol 0.078 s_similar_adp_cmpnt 0.053 s_angle_d 0.031 s_from_restr_planes 0.029 s_anti_bump_dis_restr 0.023 s_bond_d 0.014 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8195 Nucleic Acid Atoms Solvent Atoms 1432 Heterogen Atoms 37
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 CNS phasing DENZO data reduction