3AI0

Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with para-nitrophenyl-beta-D-glucopyranoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AHZPDB ENTRY 3AHZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.1M Bis-Tris, 18-21%(w/v) PEG 3350, 0.1-0.25M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1743.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.089α = 90
b = 68.755β = 95.68
c = 75.746γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210Vertically Focusing Mirror2009-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C10.97315NSRRCBL13C1

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
11.43099.50.04131.24.59369993220118.6
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)
1.41.4597.40.428349350

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 3AHZ1.425.484715449195.070.123410.121840.15304RANDOM13.103
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]
-1.04-0.3-0.321.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.826
r_dihedral_angle_4_deg12.564
r_dihedral_angle_3_deg10.29
r_sphericity_free7.032
r_dihedral_angle_1_deg5.485
r_scangle_it4.402
r_sphericity_bonded3.766
r_scbond_it3.119
r_mcangle_it2.179
r_rigid_bond_restr1.705
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.826
r_dihedral_angle_4_deg12.564
r_dihedral_angle_3_deg10.29
r_sphericity_free7.032
r_dihedral_angle_1_deg5.485
r_scangle_it4.402
r_sphericity_bonded3.766
r_scbond_it3.119
r_mcangle_it2.179
r_rigid_bond_restr1.705
r_mcbond_it1.507
r_angle_refined_deg1.431
r_chiral_restr0.111
r_gen_planes_refined0.014
r_bond_refined_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3810
Nucleic Acid Atoms
Solvent Atoms781
Heterogen Atoms27

Software

Software
Software NamePurpose
HKL-2000data collection
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing