1QMV

thioredoxin peroxidase B from red blood cells


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.516 % (V/V) PEG 400, 100 MM TRIS-HCL, PH 7.5, 10 % (V/V) 2-PROPANOL, 10 MM DITHIOERYTHREITOL
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.88α = 90
b = 107.03β = 110.87
c = 119.5γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH1998-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.72099.60.05718.84.222801034.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7393.60.4931.73

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PRX1.720225682228798.60.1920.256RANDOM32.7
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]
-7.341-1.20118.791-11.027
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor26.9
p_staggered_tor14.3
p_scangle_it5.849
p_scbond_it4.675
p_planar_tor4.2
p_mcangle_it3.071
p_mcbond_it2.467
p_multtor_nbd0.246
p_singtor_nbd0.173
p_chiral_restr0.146
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor26.9
p_staggered_tor14.3
p_scangle_it5.849
p_scbond_it4.675
p_planar_tor4.2
p_mcangle_it3.071
p_mcbond_it2.467
p_multtor_nbd0.246
p_singtor_nbd0.173
p_chiral_restr0.146
p_xyhbond_nbd0.122
p_planar_d0.031
p_angle_d0.027
p_plane_restr0.022
p_bond_d0.011
p_xhyhbond_nbd
p_hb_or_metal_coord
p_orthonormal_tor
p_angle_deg
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15440
Nucleic Acid Atoms
Solvent Atoms2194
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
MOLREPphasing
REFMACrefinement