6YC4

Crystal structure of the steady-state activated state of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6XYT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE82931.2 M NaMal pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.6466.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.189α = 90
b = 239.861β = 90
c = 138.456γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER X 16M2019-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.976PETRA III, EMBL c/o DESYP14 (MX2)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
12.5948.8199.60.2370.2520.0860.9946.78.569594
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.592.6594.82.1312.270.7710.5078.6

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6xyt2.62065587348799.630.18610.18470.2123RANDOM49.282
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]
4.56-6.081.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.042
r_dihedral_angle_3_deg9.089
r_dihedral_angle_4_deg6.007
r_dihedral_angle_1_deg2.18
r_angle_refined_deg1.077
r_angle_other_deg1.045
r_chiral_restr0.038
r_gen_planes_refined0.002
r_bond_refined_d0.001
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.042
r_dihedral_angle_3_deg9.089
r_dihedral_angle_4_deg6.007
r_dihedral_angle_1_deg2.18
r_angle_refined_deg1.077
r_angle_other_deg1.045
r_chiral_restr0.038
r_gen_planes_refined0.002
r_bond_refined_d0.001
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10769
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms741

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing