3GM8

Crystal structure of a beta-glycosidase from Bacteroides vulgatus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8294100mM Tris HCl pH 8.0, 28% PEG 3350, 150mM ammonium sulfate, vapor diffusion, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.1761.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.754α = 90
b = 193.348β = 90
c = 190.667γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97958APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.443.76998.30.1440.1448.45457964501743
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5399.20.4650.4652.956555

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.4204577944941227798.170.2290.2260.287RANDOM51.116
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]
0.580.72-1.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.894
r_dihedral_angle_4_deg19.946
r_dihedral_angle_3_deg15.209
r_dihedral_angle_1_deg6.899
r_scangle_it3.133
r_scbond_it2.027
r_angle_refined_deg1.572
r_mcangle_it1.368
r_angle_other_deg0.909
r_mcbond_it0.721
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.894
r_dihedral_angle_4_deg19.946
r_dihedral_angle_3_deg15.209
r_dihedral_angle_1_deg6.899
r_scangle_it3.133
r_scbond_it2.027
r_angle_refined_deg1.572
r_mcangle_it1.368
r_angle_other_deg0.909
r_mcbond_it0.721
r_mcbond_other0.142
r_chiral_restr0.089
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6112
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms12

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building