X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5E31ensemble of models was used: 5e31, 5dvy, 1vqq, 3ocl, 4ool, 4wek, 4wej, 4mnr, 1xkw
experimental modelPDB 5DVYensemble of models was used: 5e31, 5dvy, 1vqq, 3ocl, 4ool, 4wek, 4wej, 4mnr, 1xkw
experimental modelPDB 1VQQensemble of models was used: 5e31, 5dvy, 1vqq, 3ocl, 4ool, 4wek, 4wej, 4mnr, 1xkw
experimental modelPDB 3OCLensemble of models was used: 5e31, 5dvy, 1vqq, 3ocl, 4ool, 4wek, 4wej, 4mnr, 1xkw
experimental modelPDB 4OOLensemble of models was used: 5e31, 5dvy, 1vqq, 3ocl, 4ool, 4wek, 4wej, 4mnr, 1xkw
experimental modelPDB 4WEKensemble of models was used: 5e31, 5dvy, 1vqq, 3ocl, 4ool, 4wek, 4wej, 4mnr, 1xkw
experimental modelPDB 4WEJensemble of models was used: 5e31, 5dvy, 1vqq, 3ocl, 4ool, 4wek, 4wej, 4mnr, 1xkw
experimental modelPDB 4MNRensemble of models was used: 5e31, 5dvy, 1vqq, 3ocl, 4ool, 4wek, 4wej, 4mnr, 1xkw
experimental modelPDB 1XKWensemble of models was used: 5e31, 5dvy, 1vqq, 3ocl, 4ool, 4wek, 4wej, 4mnr, 1xkw

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.1 M TrisBase / Bicine pH 8,5 ; 0.1 M Carboxylic acids mix (0.02 M Sodium formate ; 0.02 M Ammonium acetate ; 0.02 M Sodium citrate tribasic dihydrate ; 0.02 M Sodium potassium tartrate tetrahydrate ; 0.02 M Sodium oxamate) ; 24 % Glycerol ; 12 % PEG 4000
Crystal Properties
Matthews coefficientSolvent content
3.665.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.303α = 90
b = 182.806β = 90
c = 75.561γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1245.792.840.19850.057330.9958.3211.359191
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0780.63.2543.4241.0540.5710.4

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-VALUEensemble of models was used: 5e31, 5dvy, 1vqq, 3ocl, 4ool, 4wek, 4wej, 4mnr, 1xkw2.00144.40555067186092.840.21730.21590.2596
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_d4.134
f_angle_d0.944
f_chiral_restr0.052
f_bond_d0.008
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4275
Nucleic Acid Atoms
Solvent Atoms364
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MoRDaphasing