6TK6

Femtosecond to millisecond structural changes in a light-driven sodium pump: Dark structure in neutral conditions with attached light datasets at 800fs, 2ps, 100ps, 1ns, 16ns, 1us, 30us, 150us, 1ms and 20ms


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3X3C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE4.4293200 mM Sodium Acetate pH 4.4, 150 mM MgCl2, 35% PEG 200
Crystal Properties
Matthews coefficientSolvent content
3.1460.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.54α = 90
b = 84.48β = 90
c = 235.56γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELPSI JUNGFRAU 16M2019-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSwissFEL ARAMIS BEAMLINE ESA1.0SwissFEL ARAMISESA

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1High viscosity injectorinjection
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
175capillary
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
1503.512.4

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
11.612.4377.210.04911.1132831741
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)
11.62.335.40.950.33.1872

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 REPLACEMENTTHROUGHOUT3x3c1.612.4261.3531728207757.460.18980.18790.217339.2853
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2083
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms242

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing