2WBG

Structure of family 1 beta-glucosidase from Thermotoga maritima in complex with 3-imino-2-oxa-(+)-castanospermine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OD0PDB ENTRY 1OD0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1710 MG/ML PROTEIN, 0.1 M IMIDAZOLE, PH 7, 0.2 M CALCIUM ACETATE, 14-19% PEG 4K
Crystal Properties
Matthews coefficientSolvent content
2.141

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.989α = 90
b = 73.187β = 94.03
c = 138.085γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.85201000.0913.53.9152735
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)
11.851.921000.482.73.9

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 1OD01.85137.36144968766799.660.15580.153480.19876RANDOM17.62
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]
-0.440.76-0.240.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.675
r_dihedral_angle_4_deg19.137
r_dihedral_angle_3_deg13.889
r_dihedral_angle_1_deg6.009
r_scangle_it3.541
r_scbond_it2.272
r_angle_refined_deg1.452
r_mcangle_it1.365
r_mcbond_it0.8
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.675
r_dihedral_angle_4_deg19.137
r_dihedral_angle_3_deg13.889
r_dihedral_angle_1_deg6.009
r_scangle_it3.541
r_scbond_it2.272
r_angle_refined_deg1.452
r_mcangle_it1.365
r_mcbond_it0.8
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.008
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_mcangle_other
r_scbond_other
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 Atoms14422
Nucleic Acid Atoms
Solvent Atoms1767
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing