3TJK

Crystal Structure of human peroxiredoxin IV C245A mutant in reduced form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PN8PDB ENTRY 2PN8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72891.0 M succinic acid, 1% w/v PEG2000 MME, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4249.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.24α = 90
b = 138.4β = 103.8
c = 96γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2011-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97950DiamondI02

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
12.0983.7199.60.05314.34.7805298052935.4
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)
12.092.1599.80.6832.44.75992

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 2PN82.0983.717984675828401898.720.162470.162470.160430.20125RANDOM44.952
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]
2.06-1.060.07-2.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.999
r_dihedral_angle_4_deg16.469
r_dihedral_angle_3_deg16.339
r_dihedral_angle_1_deg6.183
r_scangle_it3.949
r_scbond_it2.488
r_angle_refined_deg1.598
r_mcangle_it1.49
r_mcbond_it0.816
r_chiral_restr0.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.999
r_dihedral_angle_4_deg16.469
r_dihedral_angle_3_deg16.339
r_dihedral_angle_1_deg6.183
r_scangle_it3.949
r_scbond_it2.488
r_angle_refined_deg1.598
r_mcangle_it1.49
r_mcbond_it0.816
r_chiral_restr0.112
r_bond_refined_d0.017
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7805
Nucleic Acid Atoms
Solvent Atoms735
Heterogen Atoms

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement