☰ Navigation Tabs
Crystal structure of glucosidase II alpha subunit (DNJ-bound from)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.2 M sodium citrate tribasic, 0.1 M Tris-HCl (pH 7.0), 2.5 mM DNJ
Crystal Properties Matthews coefficient Solvent content 2.51 51.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 189.523 α = 90 b = 189.523 β = 90 c = 157.784 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 ADSC QUANTUM 270 2013-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 0.97946 Photon Factory AR-NE3A
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 1.6 50 98.3 0.086 23.6 2.8 141836 -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 1.6 1.63 98 0.419 2.8 2.6
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 1.6 20 133918 7092 99.42 0.156 0.155 0.1677 0.184 0.1943 RANDOM 20.444
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] -0.05 -0.03 -0.05 0.16
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.551 r_long_range_B_other 4.234 r_scangle_other 3.059 r_scbond_it 1.934 r_scbond_other 1.934 r_mcangle_it 1.901 r_mcangle_other 1.901 r_angle_refined_deg 1.427 r_mcbond_it 1.255 r_mcbond_other 1.253
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.551 r_long_range_B_other 4.234 r_scangle_other 3.059 r_scbond_it 1.934 r_scbond_other 1.934 r_mcangle_it 1.901 r_mcangle_other 1.901 r_angle_refined_deg 1.427 r_mcbond_it 1.255 r_mcbond_other 1.253 r_angle_other_deg 0.795 r_chiral_restr 0.087 r_bond_refined_d 0.011 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 7485 Nucleic Acid Atoms Solvent Atoms 819 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHENIX phasing