2NVK

Crystal Structure of Thioredoxin Reductase from Drosophila melanogaster


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H6V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5293200 mM Succinate, 22% PEG 6000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.856.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.487α = 90
b = 151.487β = 90
c = 134.259γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray104IMAGE PLATEMAR scanner 345 mm plateXenocs FOX-2D Multilayer Mirrors2006-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
12.41598.70.05913.27.8522987
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)
12.42.4990.30.4222.782075

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 REPLACEMENTTHROUGHOUT1H6V2.41521869220193.840.2030.1980.247RANDOM49.14
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]
1.70.851.7-2.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.685
r_dihedral_angle_4_deg19.865
r_dihedral_angle_3_deg18.707
r_dihedral_angle_1_deg6.15
r_scangle_it1.836
r_angle_refined_deg1.359
r_scbond_it1.12
r_mcangle_it0.761
r_mcbond_it0.425
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.685
r_dihedral_angle_4_deg19.865
r_dihedral_angle_3_deg18.707
r_dihedral_angle_1_deg6.15
r_scangle_it1.836
r_angle_refined_deg1.359
r_scbond_it1.12
r_mcangle_it0.761
r_mcbond_it0.425
r_nbtor_refined0.304
r_nbd_refined0.214
r_symmetry_vdw_refined0.2
r_symmetry_hbond_refined0.197
r_xyhbond_nbd_refined0.13
r_chiral_restr0.095
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3670
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing