3FDY

Pyranose 2-oxidase thermostable triple mutant, T169G/E542K/V546C


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IGOPDB ENTRY 2IGO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.229810% (w/v) monomethylether PEG 2000, 0.1M Mes pH 5.2, 50mM MgCl2, 25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3647.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.58α = 90
b = 101.58β = 90
c = 126.85γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2008-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.0MAX III911-3

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
11.5579.399.80.15912.816.41581896
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)
11.551.697.50.8852.811.396227

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2IGO1.5553.893323289999.770.187030.186020.21883RANDOM9.57
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]
-0.18-0.180.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.119
r_dihedral_angle_4_deg14.412
r_dihedral_angle_3_deg13.86
r_dihedral_angle_1_deg6.945
r_scangle_it4.069
r_scbond_it2.955
r_angle_refined_deg1.981
r_mcangle_it1.698
r_mcbond_it1.4
r_angle_other_deg1.054
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.119
r_dihedral_angle_4_deg14.412
r_dihedral_angle_3_deg13.86
r_dihedral_angle_1_deg6.945
r_scangle_it4.069
r_scbond_it2.955
r_angle_refined_deg1.981
r_mcangle_it1.698
r_mcbond_it1.4
r_angle_other_deg1.054
r_mcbond_other0.366
r_symmetry_vdw_other0.223
r_nbd_refined0.222
r_nbd_other0.215
r_chiral_restr0.208
r_symmetry_vdw_refined0.2
r_nbtor_refined0.192
r_xyhbond_nbd_refined0.168
r_symmetry_hbond_refined0.146
r_nbtor_other0.097
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4538
Nucleic Acid Atoms
Solvent Atoms470
Heterogen Atoms65

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling