1UZ4

Common inhibition of beta-glucosidase and beta-mannosidase by isofagomine lactam reflects different conformational intineraries for glucoside and mannoside hydrolysis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UUQPDB ENTRY 1UUQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.624% PEG 4000 0.2M NA ACETATE PH4.6, O.2M AMMONUM SULFATE, pH 4.60
Crystal Properties
Matthews coefficientSolvent content
2.447.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.625α = 90
b = 102.37β = 90
c = 50.356γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1202003-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.72094.90.05618.283.949493
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7695.10.5543.153.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1UUQ1.712046919253794.50.1350.1330.165RANDOM13.77
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]
-0.430.78-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.027
r_scangle_it4.111
r_scbond_it2.603
r_mcangle_it1.615
r_angle_refined_deg1.486
r_angle_other_deg0.931
r_mcbond_it0.889
r_symmetry_vdw_refined0.405
r_nbd_other0.253
r_symmetry_vdw_other0.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.027
r_scangle_it4.111
r_scbond_it2.603
r_mcangle_it1.615
r_angle_refined_deg1.486
r_angle_other_deg0.931
r_mcbond_it0.889
r_symmetry_vdw_refined0.405
r_nbd_other0.253
r_symmetry_vdw_other0.246
r_nbd_refined0.209
r_symmetry_hbond_refined0.207
r_xyhbond_nbd_refined0.189
r_chiral_restr0.104
r_nbtor_other0.083
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 AtomsNumber
Protein Atoms3308
Nucleic Acid Atoms
Solvent Atoms528
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing