4LLR

Tryparedoxin peroxidase (TXNPX) from trypanosoma cruzi in the reduced state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E2YPDB ENTRY 1E2Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5100MM EDTA, 15% PEG3350, 10% GLYCEROL, 100MM TRISHCL PH7.5, 100MM DTT, 0.25% DMSO, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
3.0960.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.555α = 90
b = 87.018β = 102.77
c = 127.144γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287CCDADSC QUANTUM 2102002-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
12.83099.90.1323.726602566025
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)
12.82.8799.70.216.443.63

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1E2Y2.829.976268562685335099.810.163610.161950.19518RANDOM30.852
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]
-0.01-0.140.15-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.839
r_dihedral_angle_3_deg20.56
r_dihedral_angle_4_deg13.286
r_dihedral_angle_1_deg6.619
r_mcangle_it3.606
r_scbond_it3.463
r_mcbond_it2.268
r_mcbond_other2.268
r_angle_refined_deg1.83
r_angle_other_deg1.695
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.839
r_dihedral_angle_3_deg20.56
r_dihedral_angle_4_deg13.286
r_dihedral_angle_1_deg6.619
r_mcangle_it3.606
r_scbond_it3.463
r_mcbond_it2.268
r_mcbond_other2.268
r_angle_refined_deg1.83
r_angle_other_deg1.695
r_chiral_restr0.111
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.009
r_gen_planes_other0.007
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15380
Nucleic Acid Atoms
Solvent Atoms453
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection