X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2957.3 mg/mL of SAD in 20 mM HEPES-KOH, 50 mM KCl, pH 7.5 was pre-mixed with NAD+ (final concentration 5 mM). The pre-mixed protein was then mixed in a 2:1 ratio with 250 mM Bis-Tris-Propane, pH 8.25, 20 % (w/v) PEG4000. The final drop size was 3 uL. The crystal was soaked with 5 mM succinic semialdehyde for 2 minutes and the drop was complemented with PEG200 to a final concentration of 20 % (v/v) before flash freezing the crystal in liquid nitrogen.
Crystal Properties
Matthews coefficientSolvent content
2.3948.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.52α = 90
b = 115.62β = 90
c = 179.64γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2023-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.9677ESRFMASSIF-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.338.0799.90.1540.163999999999999980.9989.598.485212
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.360.9981.0630.8590000000000001

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTFREE R-VALUE2.338.071.3685024199599.70.1970.19620.2278
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_d11.968
f_angle_d0.54
f_chiral_restr0.041
f_plane_restr0.004
f_bond_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13904
Nucleic Acid Atoms
Solvent Atoms461
Heterogen Atoms204

Software

Software
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing