3CMJ

Crystal Structure of engineered Beta-Glucosidase from Soil metagenome


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OIMPDB code 1OIM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7295Na/K tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0740.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.331α = 90
b = 71.002β = 90
c = 86.978γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-01-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 6C11.23986PAL/PLS6C1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.620940.06235.5755473511
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.61.660.1862.3

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 DIFFRACTIONTHROUGHOUTPDB code 1OIM1.62054699275694.160.1650.1630.198RANDOM15.931
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]
-0.350.5-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.097
r_dihedral_angle_4_deg18.971
r_dihedral_angle_1_deg12.877
r_dihedral_angle_3_deg12.591
r_scangle_it3.108
r_scbond_it1.895
r_angle_refined_deg1.341
r_mcangle_it1.118
r_mcbond_it0.58
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.097
r_dihedral_angle_4_deg18.971
r_dihedral_angle_1_deg12.877
r_dihedral_angle_3_deg12.591
r_scangle_it3.108
r_scbond_it1.895
r_angle_refined_deg1.341
r_mcangle_it1.118
r_mcbond_it0.58
r_nbtor_refined0.31
r_symmetry_vdw_refined0.215
r_nbd_refined0.211
r_chiral_restr0.128
r_xyhbond_nbd_refined0.107
r_symmetry_hbond_refined0.095
r_metal_ion_refined0.091
r_symmetry_metal_ion_refined0.074
r_bond_refined_d0.01
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3531
Nucleic Acid Atoms
Solvent Atoms367
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing