X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.72930.1 M Tris (base) bicine pH 8.6 - 8.8, 17 - 21% v/v PEG 500 MME, 8 - 10% w/v PEG 20000.Before setting up the drops 13 mg ml-1 Vc1313-LBD was mixed with 10 mM D-arginine from a 200 mM stock. The protein-ligand mixture was then mixed with reservoir solution in a 3:1 ratio. Before flash freezing the crystal in liquid nitrogen, the PEG concentrations were raised to 23% v/v PEG 500*MME, 12% w/v PEG 20000.
Crystal Properties
Matthews coefficientSolvent content
2.4850.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.499α = 75.81
b = 44.557β = 84.49
c = 55.337γ = 74.74
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 2M2021-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8731ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.937.1296.320.08640.10310.05540.9947.463.42609935.43
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)
11.91.9680.58

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONAB INITIO PHASINGFREE R-VALUE1.937.121.982608796.320.19140.224542.95
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_d4.9578
f_angle_d0.9555
f_chiral_restr0.0422
f_plane_restr0.0084
f_bond_d0.0074
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2516
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
Arcimboldophasing
PHASERphasing
Cootmodel building
XDSdata reduction
XDSdata scaling