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Crystal structure of glucosidase II alpha subunit (alpha3-Glc2-bound from)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1.2 M sodium citrate tribasic, 0.1 M Tris-HCl (pH 8.0), 5 mM alpha3-Glc2 soaking
Crystal Properties Matthews coefficient Solvent content 2.54 51.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 189.947 α = 90 b = 189.947 β = 90 c = 158.642 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD RAYONIX MX300HE 2014-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 2.4 50 100 0.093 33.5 7.5 43022 43005 -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 2.4 2.44 100 0.433 6.4 7.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 SAD THROUGHOUT 2.4 20 40816 2038 99.78 0.15 0.148 0.1563 0.199 0.2021 RANDOM 33.844
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] -0.39 -0.19 -0.39 1.26
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.809 r_long_range_B_other 4.808 r_scangle_other 4.115 r_mcangle_other 3.026 r_mcangle_it 3.025 r_scbond_it 2.463 r_scbond_other 2.463 r_mcbond_it 1.941 r_mcbond_other 1.937 r_angle_refined_deg 1.339
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.809 r_long_range_B_other 4.808 r_scangle_other 4.115 r_mcangle_other 3.026 r_mcangle_it 3.025 r_scbond_it 2.463 r_scbond_other 2.463 r_mcbond_it 1.941 r_mcbond_other 1.937 r_angle_refined_deg 1.339 r_angle_other_deg 0.756 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7427 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHENIX phasing