8Y0M | pdb_00008y0m

beta-glucosidase mutant M279V_T308S_K361R_D433N_N514C


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IIDChain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.1 M HEPES pH7.0, 0.16 M magnesium chloride, 25% 2-propanol, 0.5 mM 1-deoxynojirimycin
Crystal Properties
Matthews coefficientSolvent content
2.4349.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.195α = 90
b = 150.165β = 90
c = 174.892γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDADSC QUANTUM 2102012-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.00000Photon FactoryBL-5A

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
12.340.299.870.12411.64.17160623
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)
12.32.35999.380.052.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.340.2153281800899.870.162770.161860.1680.180240.1851RANDOM20.175
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]
-0.010.02-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.581
r_dihedral_angle_1_deg6.608
r_dihedral_angle_2_deg3.261
r_long_range_B_refined2.984
r_long_range_B_other2.984
r_mcangle_it1.12
r_mcangle_other1.12
r_angle_refined_deg1.052
r_scangle_other1.051
r_mcbond_it0.617
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.581
r_dihedral_angle_1_deg6.608
r_dihedral_angle_2_deg3.261
r_long_range_B_refined2.984
r_long_range_B_other2.984
r_mcangle_it1.12
r_mcangle_other1.12
r_angle_refined_deg1.052
r_scangle_other1.051
r_mcbond_it0.617
r_mcbond_other0.617
r_scbond_it0.578
r_scbond_other0.578
r_angle_other_deg0.397
r_chiral_restr0.053
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23904
Nucleic Acid Atoms
Solvent Atoms3002
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing