5AYI

Crystal structure of GH1 Beta-glucosidase TD2F2 N223Q mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WH5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52931.2M K/NA TARTRATE, 0.1M NA-CHES, 0.2M LI2SO4, PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.2845.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.06α = 90
b = 69.803β = 90
c = 96.335γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102014-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.000Photon FactoryAR-NW12A

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
11.85501000.13113.44.940537
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)
11.851.881000.4543.34.9

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 REPLACEMENTTHROUGHOUT3WH51.8545.9738446203099.940.141730.139950.17543RANDOM13.71
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.133
r_dihedral_angle_4_deg18.469
r_dihedral_angle_3_deg12.101
r_dihedral_angle_1_deg6.637
r_long_range_B_refined4.969
r_long_range_B_other4.969
r_scangle_other3.159
r_scbond_it2.053
r_scbond_other2.051
r_mcangle_it1.946
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.133
r_dihedral_angle_4_deg18.469
r_dihedral_angle_3_deg12.101
r_dihedral_angle_1_deg6.637
r_long_range_B_refined4.969
r_long_range_B_other4.969
r_scangle_other3.159
r_scbond_it2.053
r_scbond_other2.051
r_mcangle_it1.946
r_mcangle_other1.945
r_angle_refined_deg1.847
r_mcbond_it1.329
r_mcbond_other1.329
r_angle_other_deg1.091
r_chiral_restr0.131
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.006
r_gen_planes_other0.001
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 Atoms3470
Nucleic Acid Atoms
Solvent Atoms378
Heterogen Atoms38

Software

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