3FD6

Crystal structure of human selenophosphate synthetase 1 complex with ADP and phosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293100mM HEPES-NaOH pH 7.0, 50mM MgCl2, 30% PEGMME550, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4249.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.618α = 90
b = 67.618β = 90
c = 182.551γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 6000MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.955093.25710353229-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.951.9851.8

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.9514.960.0352680200888.890.13290.13050.1957RANDOM
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]
-5.045-5.045-4.37
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.16
f_angle_d1.312
f_chiral_restr0.078
f_bond_d0.01
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5193
Nucleic Acid Atoms
Solvent Atoms534
Heterogen Atoms72

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
PHENIXmodel building
PHENIXrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing