4HA3

Structure of beta-glycosidase from Acidilobus saccharovorans in complex with Tris


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GOW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293Protein solution (1.5mcl): 15mg/ml Asbeta-Gly, 0.025M NaCl, 0.05M Tris (pH 8.0). Reservoir solution (1.5mcl): 0.04M cellobiose, 0.16M magnesium acetate, 0.08M sodium cacodylate (pH 6.5), 16% w/v polyethylene glycol 8000, 20% v/v glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6553.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.18α = 90
b = 84.18β = 90
c = 166.22γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2010-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONKURCHATOV SNC BEAMLINE K4.40.9779KURCHATOV SNCK4.4

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
11.4619.841980.06326.810205010205020.3
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)
11.461.5591.10.5194.515340

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 REPLACEMENTTHROUGHOUT1gow1.4619.84196870510997.960.143940.143140.15886RANDOM14.262
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]
-0.26-0.260.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.266
r_dihedral_angle_4_deg16.422
r_dihedral_angle_3_deg11.759
r_dihedral_angle_1_deg6.175
r_scangle_it3.081
r_scbond_it1.975
r_angle_refined_deg1.531
r_mcangle_it1.337
r_angle_other_deg0.882
r_mcbond_it0.774
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.266
r_dihedral_angle_4_deg16.422
r_dihedral_angle_3_deg11.759
r_dihedral_angle_1_deg6.175
r_scangle_it3.081
r_scbond_it1.975
r_angle_refined_deg1.531
r_mcangle_it1.337
r_angle_other_deg0.882
r_mcbond_it0.774
r_mcbond_other0.228
r_chiral_restr0.099
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3906
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms38

Software

Software
Software NamePurpose
AUTOMARdata collection
BALBESphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling