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Crystal structure of acid-beta-glucosidase with isofagomine at neutral pH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NSX PDB entry '2NSX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 298 0.8 M NaH2PO4, 0.8 M KH2PO4, 0.1 M Hepes pH 7.5,
SOAK with 500uM isofagomine for 10 min,
glycerol in cryo, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.24 62.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.311 α = 90 b = 92.013 β = 111.21 c = 152.362 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 32.12 103572
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT PDB entry '2NSX 2.4 32.12 98363 103572 5209 93.17 0.182 0.178 0.1783 0.245 0.2433 RANDOM 27.274
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] 0.2 -0.17 -0.18 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.898 r_dihedral_angle_4_deg 20.705 r_dihedral_angle_3_deg 17.889 r_dihedral_angle_1_deg 8.265 r_scangle_it 3.684 r_scbond_it 2.398 r_angle_refined_deg 1.957 r_mcangle_it 1.659 r_mcbond_it 0.978 r_xyhbond_nbd_refined 0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.898 r_dihedral_angle_4_deg 20.705 r_dihedral_angle_3_deg 17.889 r_dihedral_angle_1_deg 8.265 r_scangle_it 3.684 r_scbond_it 2.398 r_angle_refined_deg 1.957 r_mcangle_it 1.659 r_mcbond_it 0.978 r_xyhbond_nbd_refined 0.335 r_nbtor_refined 0.313 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.198 r_symmetry_hbond_refined 0.184 r_chiral_restr 0.134 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15720 Nucleic Acid Atoms Solvent Atoms 905 Heterogen Atoms 426
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction