5Y4T

Crystal structure of Trx domain of Grx3 from Saccharomyces cerevisiae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8289.150.1 M Tris-HCl, pH 8.0, 2 M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.0138.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.329α = 90
b = 77.329β = 90
c = 37.113γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U11.5418SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.45099.6406.922509
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)
11.4031.4496.440.0460.0462.86.9

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 REPLACEMENTTHROUGHOUT3D6I1.434.5821310115299.40.190040.188510.21907RANDOM20.83
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_deg37.785
r_dihedral_angle_3_deg13.623
r_long_range_B_refined6.278
r_long_range_B_other6.271
r_scangle_other5.484
r_dihedral_angle_1_deg4.786
r_scbond_it3.908
r_scbond_other3.889
r_mcangle_other2.577
r_mcangle_it2.576
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.785
r_dihedral_angle_3_deg13.623
r_long_range_B_refined6.278
r_long_range_B_other6.271
r_scangle_other5.484
r_dihedral_angle_1_deg4.786
r_scbond_it3.908
r_scbond_other3.889
r_mcangle_other2.577
r_mcangle_it2.576
r_angle_refined_deg2.409
r_mcbond_it1.884
r_mcbond_other1.874
r_angle_other_deg0.987
r_chiral_restr0.134
r_bond_refined_d0.03
r_gen_planes_refined0.012
r_bond_other_d0.002
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 Atoms922
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms12

Software

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