3VIM

Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with a new glucopyranosidic product


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 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
2.1542.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.124α = 90
b = 68.557β = 95.72
c = 75.455γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rVertically Collimating Premirror, Toroidal Focusing Mirror2009-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B10.80000NSRRCBL13B1

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
11.033096.40.045314.8231935223573110
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)
11.031.0794.50.5362.54.623105

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 REPLACEMENTTHROUGHOUT3AHZ1.0319.22234391121896.230.128320.127540.14299RANDOM11.694
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]
-0.47-0.31-0.130.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.362
r_dihedral_angle_4_deg14.011
r_dihedral_angle_3_deg11.031
r_dihedral_angle_1_deg5.95
r_scangle_it3.495
r_scbond_it2.41
r_mcangle_it1.696
r_angle_refined_deg1.382
r_mcbond_it1.17
r_rigid_bond_restr1.142
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.362
r_dihedral_angle_4_deg14.011
r_dihedral_angle_3_deg11.031
r_dihedral_angle_1_deg5.95
r_scangle_it3.495
r_scbond_it2.41
r_mcangle_it1.696
r_angle_refined_deg1.382
r_mcbond_it1.17
r_rigid_bond_restr1.142
r_chiral_restr0.098
r_gen_planes_refined0.009
r_bond_refined_d0.006
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3810
Nucleic Acid Atoms
Solvent Atoms651
Heterogen Atoms34

Software

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