8HH0

Peroxiredoxin from Thermococcus kodakaraensis (TkPrx) F42C/C46S/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrx*F42C)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6IU0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.2 M ammonium acetate 0.1 M sodium acetate (pH 4.6) 30% w/v polyethylene glycol 4,000
Crystal Properties
Matthews coefficientSolvent content
2.2545.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.09α = 90
b = 61.09β = 90
c = 236.919γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1SPring-8BL45XU

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
12.3548.36799.90.1660.9856.4619657
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)
12.352.430.6030.816

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6IU02.3548.36719631102199.7970.2070.20490.252952.349
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]
-0.195-0.1950.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.362
r_dihedral_angle_3_deg19.004
r_dihedral_angle_4_deg18.767
r_lrange_it7.678
r_lrange_other7.668
r_dihedral_angle_1_deg7.268
r_scangle_it6.408
r_scangle_other6.406
r_mcangle_it5.038
r_mcangle_other5.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.362
r_dihedral_angle_3_deg19.004
r_dihedral_angle_4_deg18.767
r_lrange_it7.678
r_lrange_other7.668
r_dihedral_angle_1_deg7.268
r_scangle_it6.408
r_scangle_other6.406
r_mcangle_it5.038
r_mcangle_other5.038
r_scbond_it4.326
r_scbond_other4.325
r_mcbond_it3.738
r_mcbond_other3.73
r_angle_refined_deg1.548
r_angle_other_deg1.227
r_symmetry_nbd_refined0.256
r_nbd_refined0.194
r_nbd_other0.194
r_symmetry_nbd_other0.186
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.163
r_symmetry_xyhbond_nbd_refined0.158
r_symmetry_xyhbond_nbd_other0.096
r_symmetry_nbtor_other0.077
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3436
Nucleic Acid Atoms
Solvent Atoms46
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing