2ZXE

Crystal structure of the sodium - potassium pump in the E2.2K+.Pi state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B8E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Dialysis7298pH 7.0, Dialysis, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0860.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 223.815α = 90
b = 50.914β = 105.12
c = 163.786γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
21CCDRAYONIX MX225HE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.9SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.45099.10.05838.8177071070074
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4695.70.3722.85.85155

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT3B8E2.4156615735551000.247720.246440.27124RANDOM59.782
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]
2.05-1.990.01-3.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.775
r_dihedral_angle_4_deg15.787
r_dihedral_angle_3_deg14.955
r_dihedral_angle_1_deg4.084
r_scangle_it1.467
r_angle_refined_deg1.085
r_mcangle_it1.032
r_scbond_it0.863
r_mcbond_it0.564
r_chiral_restr0.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.775
r_dihedral_angle_4_deg15.787
r_dihedral_angle_3_deg14.955
r_dihedral_angle_1_deg4.084
r_scangle_it1.467
r_angle_refined_deg1.085
r_mcangle_it1.032
r_scbond_it0.863
r_mcbond_it0.564
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10131
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing