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Structure of acid-beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 1 M Ammonium Sulfate
0.17 M Guanidinium HCl
0.02 M KCl
0.1 M Acetate buffer pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.22 61.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.967 α = 90 b = 92.216 β = 110.94 c = 152.67 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 MARRESEARCH 2005-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 50 91.5 0.078 13.1 3.8 149310 149310 36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 70.4 0.356 3 3.3 11457
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 1OGS 2.11 50 141806 7504 91.27 0.19319 0.191 0.1911 0.23492 0.233 RANDOM 36.102
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] 4.93 -0.71 -3 -2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.21 r_dihedral_angle_4_deg 21.739 r_dihedral_angle_3_deg 16.335 r_dihedral_angle_1_deg 6.878 r_scangle_it 3.175 r_scbond_it 2.089 r_angle_refined_deg 1.527 r_mcangle_it 1.45 r_mcbond_it 0.887 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.21 r_dihedral_angle_4_deg 21.739 r_dihedral_angle_3_deg 16.335 r_dihedral_angle_1_deg 6.878 r_scangle_it 3.175 r_scbond_it 2.089 r_angle_refined_deg 1.527 r_mcangle_it 1.45 r_mcbond_it 0.887 r_nbtor_refined 0.31 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.106 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15720 Nucleic Acid Atoms Solvent Atoms 1006 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling