3AHZ

Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with Tris


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CBGPDB ENTRY 1CBG

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
2.1442.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.959α = 90
b = 68.451β = 95.53
c = 75.228γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateVertically Focusing Mirror2008-08-16MSINGLE 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
11.343099.90.05429.75.7105275105222116.2
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)
1.341.3999.70.4693.95.510460

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 1CBG1.3425.695986506196.070.116710.115260.14381RANDOM11.842
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]
-0.65-0.58-0.20.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.012
r_dihedral_angle_4_deg13.711
r_dihedral_angle_3_deg10.651
r_sphericity_free7.024
r_dihedral_angle_1_deg5.88
r_scangle_it4.221
r_sphericity_bonded3.569
r_scbond_it2.996
r_mcangle_it2.113
r_rigid_bond_restr1.607
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.012
r_dihedral_angle_4_deg13.711
r_dihedral_angle_3_deg10.651
r_sphericity_free7.024
r_dihedral_angle_1_deg5.88
r_scangle_it4.221
r_sphericity_bonded3.569
r_scbond_it2.996
r_mcangle_it2.113
r_rigid_bond_restr1.607
r_angle_refined_deg1.525
r_mcbond_it1.469
r_chiral_restr0.101
r_gen_planes_refined0.01
r_bond_refined_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3811
Nucleic Acid Atoms
Solvent Atoms806
Heterogen Atoms14

Software

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