7YEB

TR-SFX MmCPDII-DNA complex: 3.35 ns snapshot. Includes 3.35 ns, dark, and extrapolated structure factors


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE4.6296100 mM Sodium Acetate pH 4.6 250 mM ammonium sulfate 4% PEG4000 (w/v) 50 mM DTT
Crystal Properties
Matthews coefficientSolvent content
2.7855.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.47α = 90
b = 115.93β = 90
c = 169.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELPSI JUNGFRAU 16M2021-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSwissFEL ARAMIS BEAMLINE ESA1.0875SwissFEL ARAMISESA

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
1SwissFEL injector4.220
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
1100
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
180479

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.1216.7499.990.99611.091073.481528
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.122.141000.5651.99577.9

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7YC72.216.7472967357799.990.23230.23140.2499
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_d20.646
f_angle_d0.744
f_chiral_restr0.142
f_bond_d0.019
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7056
Nucleic Acid Atoms1021
Solvent Atoms373
Heterogen Atoms111

Software

Software
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
pointlessdata scaling
REFMACphasing