2ZOX

Crystal Structure of the Covalent Intermediate of Human Cytosolic beta-Glucosidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E9L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529830% PEG 3350, 0.2M MgCl2, 0.1M Tris-HCl, 15% glycerol saturated concentration of pNP-Glc , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3347.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.12α = 90
b = 82.529β = 90
c = 91.673γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.000SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.95098.30.0920.09219.44.73919439194
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9286.90.4280.4281.8

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 REPLACEMENTTHROUGHOUT2E9L1.930.6737229196498.060.192330.190570.22578RANDOM26.422
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.762
r_dihedral_angle_4_deg17.175
r_dihedral_angle_3_deg13.748
r_dihedral_angle_1_deg6.12
r_scangle_it2.165
r_scbond_it1.381
r_angle_refined_deg1.146
r_mcangle_it0.925
r_mcbond_it0.557
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.762
r_dihedral_angle_4_deg17.175
r_dihedral_angle_3_deg13.748
r_dihedral_angle_1_deg6.12
r_scangle_it2.165
r_scbond_it1.381
r_angle_refined_deg1.146
r_mcangle_it0.925
r_mcbond_it0.557
r_nbtor_refined0.307
r_symmetry_vdw_refined0.226
r_nbd_refined0.19
r_symmetry_hbond_refined0.187
r_xyhbond_nbd_refined0.117
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3778
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms101

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing