3EYT

Crystal structure of Thioredoxin-like superfamily protein SPOA0173


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62890.2M Ammonium sulfate 0.1M Sodium acetate pH 4.6 12% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4750.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.543α = 90
b = 76.8β = 90
c = 137.137γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRROR2008-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97928APS19-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
11.9568.5299.90.1420.14220.2567.15110751070-324.6
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)
11.951.97970.8930.8931.761263

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.9568.525093250932258599.660.1750.1750.1730.21RANDOM21.98
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]
1.260.31-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.663
r_dihedral_angle_4_deg17.526
r_dihedral_angle_3_deg13.321
r_dihedral_angle_1_deg5.547
r_scangle_it4.308
r_scbond_it2.693
r_angle_refined_deg1.417
r_mcangle_it1.356
r_mcbond_it0.749
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.663
r_dihedral_angle_4_deg17.526
r_dihedral_angle_3_deg13.321
r_dihedral_angle_1_deg5.547
r_scangle_it4.308
r_scbond_it2.693
r_angle_refined_deg1.417
r_mcangle_it1.356
r_mcbond_it0.749
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4735
Nucleic Acid Atoms
Solvent Atoms519
Heterogen Atoms24

Software

Software
Software NamePurpose
SBC-Collectdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
ARPmodel building
Cootmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing