X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QR6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295Crystals were grown in the presence of XMP and NAD+ in mother liquor from the condition 1-10 of the commercial screen Morpheus (Molecular Dimensions), which consists of a salt mixture (0.03M Magnesium chloride hexahydrate and 0.03M Calcium chloride dihydrate), a precipitant mix (20% v/v Ethylene glycol and 10 % w/v PEG 8000), and 0.1M of a buffer system (Tris-base, Bicine) adjusted at pH 8.5. Initial concentrations: Protein = 12.5 mg/mL XMP = 3 mM NAD = 3 mM
Crystal Properties
Matthews coefficientSolvent content
2.346.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.98α = 90
b = 131.68β = 90
c = 182.495γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979263470491ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8849.0490.40.0730.99914.214.621924331.06
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.9335.30.8060.550.671.18

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-VALUE1.8849.041.342191731104690.40.17930.17840.196734.88
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_d11.7327
f_angle_d0.684
f_chiral_restr0.0502
f_plane_restr0.0054
f_bond_d0.0048
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms22122
Nucleic Acid Atoms
Solvent Atoms1606
Heterogen Atoms376

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing