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X-RAY STRUCTURE OF ACID-BETA-GLUCOSIDASE WITH 5N,6S-(N'-(N-OCTYL)IMINO)-6-THIONOJIRIMYCIN IN THE ACTIVE SITE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J25 PDB ENTRY 2J25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2N (NH4)2SO4, 0.1M TRIS PH 6.5, 25% W/V PEG3350
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.142 α = 90 b = 96.693 β = 102.84 c = 82.97 γ = 90
Symmetry Space Group P 1 21 1
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 315r 2009-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.31 19.8 96.5 0.15 33.6 7.2 42172 2
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 2.31 2.37 86.4 0.45 9.6 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2J25 2.31 19.82 42172 2234 96.5 0.15313 0.14994 0.1502 0.21337 0.2109 RANDOM 21.341
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.86 r_dihedral_angle_4_deg 23.073 r_dihedral_angle_3_deg 15.594 r_dihedral_angle_1_deg 7.231 r_scangle_it 4.66 r_scbond_it 3.149 r_mcangle_it 1.864 r_angle_refined_deg 1.861 r_mcbond_it 1.026 r_chiral_restr 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.86 r_dihedral_angle_4_deg 23.073 r_dihedral_angle_3_deg 15.594 r_dihedral_angle_1_deg 7.231 r_scangle_it 4.66 r_scbond_it 3.149 r_mcangle_it 1.864 r_angle_refined_deg 1.861 r_mcbond_it 1.026 r_chiral_restr 0.123 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7803 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing