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Golgi alpha-mannosidase II complex with 5-thio-D-mannopyranosylamidinium salt
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 7 295 PEG 6000, Tris, MPD, NaCl, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.18 43.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.774 α = 90 b = 109.568 β = 90 c = 138.737 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 IMAGE PLATE MARRESEARCH OSMIC 2002-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.95 30 94.8 0.1012 12.2 4.2 77853 73805 2 3 6.3
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 1.95 2.02 95 0.378 3.14
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 1.95 29.25 2 73744 70924 2143 91.9 0.152 0.151 0.151 0.1509 0.196 0.1962 RANDOM 15.4
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] 0.94 0.21 -1.15
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_scangle_it 3.59 c_scbond_it 2.57 c_mcangle_it 2.18 c_angle_deg 1.9 c_mcbond_it 1.6 c_improper_angle_d 1.23 c_bond_d 0.02
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8181 Nucleic Acid Atoms Solvent Atoms 1058 Heterogen Atoms 44
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing