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Golgi alpha-mannosidase II complex with benzyl-aminocyclopentitetrol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 Tris, PEG 6K, MPD, NaCl, pH 7, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.682 α = 90 b = 109.143 β = 90 c = 138.348 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 2004-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9760 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 1.35 29.21 93.8 0.083 17.5 6.2 226440 212500 1 1 13.3
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 1.35 1.38 85.5 0.501 3.8 5 14095
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1HTY 1.35 29.21 2 227523 207592 4637 91.2 0.166 0.164 0.164 0.1669 0.186 0.1882 RANDOM 16.1
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] -1.26 0.03 1.24
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.5 c_scangle_it 3.36 c_scbond_it 2.2 c_angle_deg 2 c_mcangle_it 1.76 c_improper_angle_d 1.46 c_mcbond_it 1.12 c_bond_d 0.021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8181 Nucleic Acid Atoms Solvent Atoms 1229 Heterogen Atoms 40
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing