2R37

Crystal structure of human glutathione peroxidase 3 (selenocysteine to glycine mutant)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82770.1M PCB pH 8.0, 60% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3963.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.72α = 90
b = 61.308β = 90
c = 100.4γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00721SLSX10SA

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
11.8538.8499.90.0860.09912.54.12264252261992
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)
11.851.951000.6640.7632.34.17975

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 2I3Y1.85385539852544280799.910.152690.15110.18263RANDOM21.621
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]
0.75-0.27-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.123
r_dihedral_angle_4_deg16.304
r_dihedral_angle_3_deg12.516
r_scangle_it8.75
r_scbond_it6.272
r_dihedral_angle_1_deg6.239
r_mcangle_it3.834
r_mcbond_it2.52
r_angle_refined_deg1.414
r_angle_other_deg1.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.123
r_dihedral_angle_4_deg16.304
r_dihedral_angle_3_deg12.516
r_scangle_it8.75
r_scbond_it6.272
r_dihedral_angle_1_deg6.239
r_mcangle_it3.834
r_mcbond_it2.52
r_angle_refined_deg1.414
r_angle_other_deg1.2
r_mcbond_other0.846
r_symmetry_vdw_other0.256
r_nbd_refined0.21
r_nbd_other0.187
r_nbtor_refined0.187
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.151
r_metal_ion_refined0.094
r_symmetry_vdw_refined0.093
r_chiral_restr0.092
r_nbtor_other0.089
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
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 Atoms3013
Nucleic Acid Atoms
Solvent Atoms406
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing