7B02

Thioredoxin glutathione reductase from Schistosoma mansoni in complex with 4-Hydroxy-7-methyl-1,8-naphthyridine-3-carboxylic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V6O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729420% PEG 3350, 0,2M potassium iodide, 0,1M Bis-TRIS, 5mM DTT
Crystal Properties
Matthews coefficientSolvent content
3.0159.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.834α = 90
b = 102.439β = 112.81
c = 58.924γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.4539.9398.60.0530.9989.23.6135935
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4786.10.4830.631.9

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 REPLACEMENTTHROUGHOUT2V6O1.4539.93129182675298.510.14050.13880.1734RANDOM19.252
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]
-0.290.06-0.270.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.86
r_dihedral_angle_4_deg16.454
r_dihedral_angle_3_deg12.7
r_dihedral_angle_1_deg6.912
r_rigid_bond_restr4.169
r_angle_refined_deg2.008
r_angle_other_deg1.581
r_chiral_restr0.118
r_bond_refined_d0.017
r_gen_planes_refined0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.86
r_dihedral_angle_4_deg16.454
r_dihedral_angle_3_deg12.7
r_dihedral_angle_1_deg6.912
r_rigid_bond_restr4.169
r_angle_refined_deg2.008
r_angle_other_deg1.581
r_chiral_restr0.118
r_bond_refined_d0.017
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4530
Nucleic Acid Atoms
Solvent Atoms671
Heterogen Atoms103

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing