6YC0

Crystal structure of the steady-state-SMX 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
3.6566.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.21α = 90
b = 240.34β = 90
c = 138.37γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS3 S 6M2019-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)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
12.569.191000.9880.15211.3894.577967
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.541000.4881.50.72640.6

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 REPLACEMENTTHROUGHOUT6xyt2.750.0158999306799.960.1930.19160.2201RANDOM60.461
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]
5.95-9.073.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.264
r_dihedral_angle_3_deg8.98
r_dihedral_angle_4_deg5.865
r_dihedral_angle_1_deg2.111
r_angle_refined_deg1.075
r_angle_other_deg1.041
r_chiral_restr0.037
r_gen_planes_refined0.002
r_bond_refined_d0.001
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.264
r_dihedral_angle_3_deg8.98
r_dihedral_angle_4_deg5.865
r_dihedral_angle_1_deg2.111
r_angle_refined_deg1.075
r_angle_other_deg1.041
r_chiral_restr0.037
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
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
MOLREPphasing