3RIL

The acid beta-glucosidase active site exhibits plasticity in binding 3,4,5,6-tetrahydroxyazepane-based inhibitors: implications for pharmacological chaperone design for gaucher disease


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629811-12% PEG 3350, 0.18-0.205 M ammonium sulfate, and 0.1 M acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
3.261.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.217α = 90
b = 91.425β = 110.95
c = 152.659γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 300 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.444.540.1052.6100648

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRigid Body RefinementTHROUGHOUT2.444.54100647529296.270.173830.170720.23233RANDOM24.99
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.125
r_dihedral_angle_4_deg21.428
r_dihedral_angle_3_deg16.378
r_dihedral_angle_1_deg7.141
r_angle_refined_deg1.805
r_scangle_it0.665
r_mcangle_it0.398
r_scbond_it0.375
r_mcbond_it0.215
r_chiral_restr0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.125
r_dihedral_angle_4_deg21.428
r_dihedral_angle_3_deg16.378
r_dihedral_angle_1_deg7.141
r_angle_refined_deg1.805
r_scangle_it0.665
r_mcangle_it0.398
r_scbond_it0.375
r_mcbond_it0.215
r_chiral_restr0.12
r_bond_refined_d0.015
r_gen_planes_refined0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15700
Nucleic Acid Atoms
Solvent Atoms1184
Heterogen Atoms280

Software

Software
Software NamePurpose
SERGUIdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing