6YV2

STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH A PYRROLIDINE-3-CARBOXYLIC ACID FRAGMENT 598


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4UZ1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42951.4 M AMMONIUM SULPHATE, 0.1 M CITRIC ACID, PH 4.0
Crystal Properties
Matthews coefficientSolvent content
1.9737.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.3α = 90
b = 73.02β = 90
c = 79.46γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

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
11.8979.5199.90.127111.511.92831136.12
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)
11.891.9298.40.35216.8

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 REPLACEMENTFREE R-VALUE4UZ12.136.511.3419997111696.420.21340.21260.226347.81
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_d24.4421
f_angle_d0.6456
f_chiral_restr0.0528
f_plane_restr0.0039
f_bond_d0.0034
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2861
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms55

Software

Software
Software NamePurpose
PHENIXrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing