3WQ8

Monomer structure of hyperthermophilic beta-glucosidase mutant forming a dodecameric structure in the crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WDP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.62930.1M HEPES-NaOH pH7.6, 0.2M Ca-Acetate, 20% PEG 3350, 5% Ethyleneglycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.957.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.365α = 120.08
b = 148.872β = 94
c = 148.563γ = 99.7
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252013-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

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
12.8148.280.1128.7170856

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 REPLACEMENTTHROUGHOUT3WDP2.8148.28156940829896.440.24460.242990.27497RANDOM61.032
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]
-2.38-0.430.010.590.30.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.664
r_dihedral_angle_3_deg16.414
r_dihedral_angle_4_deg15.752
r_dihedral_angle_1_deg6.106
r_angle_refined_deg1.48
r_angle_other_deg1.444
r_chiral_restr0.082
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.664
r_dihedral_angle_3_deg16.414
r_dihedral_angle_4_deg15.752
r_dihedral_angle_1_deg6.106
r_angle_refined_deg1.48
r_angle_other_deg1.444
r_chiral_restr0.082
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.009
r_gen_planes_other0.009
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms43636
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling