7BT2

Crystal structure of the SERCA2a in the E2.ATP state


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22835% glycerol, 20-23% PEG1500, 5 mM MgSO4, 6 mM EGTA, 6% 2-methyl-2,4-pentanediol (MPD) and 100 mM MOPS pH 7.2
Crystal Properties
Matthews coefficientSolvent content
3.6466.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.604α = 90
b = 270.382β = 90
c = 97.34γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray40PIXELDECTRIS PILATUS3 6M2016-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.63097.90.0970.1030.99519.69.44856365.0535037813
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6888.20.8560.980.5771.33.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3AR43.0000284952414.98793172552.0012586532431360156897.12887539880.1939393054160.1924445440890.222002563214117
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.4099805954
f_angle_d1.10742163013
f_chiral_restr0.302679907466
f_bond_d0.00648257671243
f_plane_restr0.00582423078848
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7639
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms128

Software

Software
Software NamePurpose
DENZOdata reduction
PHENIXrefinement
SCALEPACKdata scaling
CNSphasing
CNSrefinement