2PN8

Crystal structure of human peroxiredoxin 4 (thioredoxin peroxidase)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QMVPDB entry 1QMV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M HEPES pH 7.5, 10% PEG 10000, 8% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9358

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.188α = 90
b = 138.776β = 104.52
c = 108.989γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.95370SLSX10SA

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
11.85099.010.1030.1210.13.8255385252831220.6
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)
1.81.998.30.5780.6752.33.836549

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 REPLACEMENTTHROUGHOUTPDB entry 1QMV1.8502528312528311268499.010.152770.152770.151080.18454RANDOM14.209
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]
-1.14-0.480.330.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.436
r_dihedral_angle_4_deg15.297
r_dihedral_angle_3_deg11.243
r_scangle_it7.343
r_dihedral_angle_1_deg6.237
r_scbond_it5.02
r_mcangle_it3.438
r_mcbond_it2.657
r_angle_refined_deg1.327
r_angle_other_deg0.919
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.436
r_dihedral_angle_4_deg15.297
r_dihedral_angle_3_deg11.243
r_scangle_it7.343
r_dihedral_angle_1_deg6.237
r_scbond_it5.02
r_mcangle_it3.438
r_mcbond_it2.657
r_angle_refined_deg1.327
r_angle_other_deg0.919
r_mcbond_other0.789
r_symmetry_vdw_other0.255
r_nbd_refined0.196
r_nbd_other0.195
r_nbtor_refined0.18
r_symmetry_hbond_refined0.152
r_xyhbond_nbd_refined0.15
r_symmetry_vdw_refined0.126
r_chiral_restr0.086
r_nbtor_other0.083
r_bond_refined_d0.011
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15435
Nucleic Acid Atoms
Solvent Atoms2183
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing