3L4N

Crystal structure of yeast monothiol glutaredoxin Grx6


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.528919% polyethylene glycol monomethyl ether 5000, 0.1M 2-(N-morpholino)-ethane sulfonic acid (MES), pH 6.5, 10mM reduced glutathione (GSH), VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.8957.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.556α = 90
b = 57.132β = 90
c = 59.095γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2008-11-13MSAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9795APS14-BM-C

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
11.55096.70.07735.139.327154
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)
11.51.5394.10.6712.267.31301

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.525.7225588136296.250.180510.179420.20035RANDOM18.566
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]
-0.240.54-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.219
r_dihedral_angle_3_deg10.159
r_dihedral_angle_4_deg7.27
r_dihedral_angle_1_deg5.711
r_sphericity_free3.328
r_scangle_it2.815
r_sphericity_bonded2.776
r_scbond_it2.442
r_rigid_bond_restr2.307
r_mcangle_it1.343
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.219
r_dihedral_angle_3_deg10.159
r_dihedral_angle_4_deg7.27
r_dihedral_angle_1_deg5.711
r_sphericity_free3.328
r_scangle_it2.815
r_sphericity_bonded2.776
r_scbond_it2.442
r_rigid_bond_restr2.307
r_mcangle_it1.343
r_angle_refined_deg1.23
r_mcbond_it1.089
r_nbtor_refined0.303
r_nbd_refined0.202
r_symmetry_vdw_refined0.124
r_xyhbond_nbd_refined0.098
r_chiral_restr0.097
r_symmetry_hbond_refined0.061
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms913
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms20

Software

Software
Software NamePurpose
MAR345dtbdata collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling