3ABZ

Crystal structure of Se-Met labeled Beta-glucosidase from Kluyveromyces marxianus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.1293potassium dihydrogen phosphate, PEG 8000, glycerol, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6753.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 245.678α = 90
b = 148.639β = 112.95
c = 119.779γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702008-03-03MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.97831, 0.97928, 0.96405Photon FactoryBL-17A

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
12.15501000.07220.13.821369931.8
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)
12.152.331000.2983.13.8

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 DIFFRACTIONMADTHROUGHOUT2.15502028831072499.850.162950.160060.21762RANDOM32.682
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]
0.510.49-0.670.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.31
r_dihedral_angle_4_deg17.811
r_dihedral_angle_3_deg15.887
r_dihedral_angle_1_deg6.934
r_scangle_it4.514
r_scbond_it2.981
r_mcangle_it2.05
r_angle_refined_deg1.755
r_mcbond_it1.242
r_chiral_restr0.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.31
r_dihedral_angle_4_deg17.811
r_dihedral_angle_3_deg15.887
r_dihedral_angle_1_deg6.934
r_scangle_it4.514
r_scbond_it2.981
r_mcangle_it2.05
r_angle_refined_deg1.755
r_mcbond_it1.242
r_chiral_restr0.132
r_bond_refined_d0.022
r_gen_planes_refined0.009
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 Atoms26028
Nucleic Acid Atoms
Solvent Atoms3078
Heterogen Atoms48

Software

Software
Software NamePurpose
ADSCdata collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling