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Crystal structure of glucosidase II alpha subunit (Glc1Man2-bound from)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1.2 M sodium citrate tribasic and 0.1 M Tris-HCl (pH 8.0), 5 mM Glc1Man2
Crystal Properties Matthews coefficient Solvent content 2.53 51.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 189.72 α = 90 b = 189.72 β = 90 c = 158.345 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 2.3 50 100 0.108 31.6 7.5 48696 48681 -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 2.3 2.34 100 0.457 7.2 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 2.3 20 45997 2430 99.81 0.146 0.144 0.1534 0.189 0.1913 RANDOM 25.866
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] -0.21 -0.11 -0.21 0.69
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.73 r_long_range_B_other 4.705 r_scangle_other 4.09 r_mcangle_other 2.783 r_mcangle_it 2.782 r_scbond_it 2.42 r_scbond_other 2.419 r_mcbond_it 1.748 r_mcbond_other 1.744 r_angle_refined_deg 1.453
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.73 r_long_range_B_other 4.705 r_scangle_other 4.09 r_mcangle_other 2.783 r_mcangle_it 2.782 r_scbond_it 2.42 r_scbond_other 2.419 r_mcbond_it 1.748 r_mcbond_other 1.744 r_angle_refined_deg 1.453 r_angle_other_deg 0.784 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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 7446 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHENIX phasing