2HT9

The structure of dimeric human glutaredoxin 2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52931.6M MgSO4, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6753.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.754α = 90
b = 111.754β = 90
c = 51.647γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.976SLSX10SA

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
11.896.67491.70.0650.0657.33.9264172641727
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)
11.9287.10.4160.4161.83.13637

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2fls1.996.672640425063134190.380.1510.150880.149390.17829RANDOM26.188
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]
0.80.40.8-1.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.085
r_sphericity_bonded15.612
r_dihedral_angle_3_deg12.937
r_dihedral_angle_4_deg11.432
r_scangle_it9.199
r_scbond_it6.98
r_rigid_bond_restr6.261
r_dihedral_angle_1_deg5.975
r_mcangle_it4.404
r_mcbond_it3.467
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.085
r_sphericity_bonded15.612
r_dihedral_angle_3_deg12.937
r_dihedral_angle_4_deg11.432
r_scangle_it9.199
r_scbond_it6.98
r_rigid_bond_restr6.261
r_dihedral_angle_1_deg5.975
r_mcangle_it4.404
r_mcbond_it3.467
r_angle_refined_deg1.448
r_mcbond_other1.046
r_angle_other_deg0.971
r_nbd_refined0.201
r_nbd_other0.179
r_nbtor_refined0.173
r_symmetry_vdw_other0.167
r_xyhbond_nbd_refined0.148
r_symmetry_vdw_refined0.138
r_symmetry_hbond_refined0.122
r_nbtor_other0.085
r_chiral_restr0.084
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
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_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1755
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms44

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling