X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5V1J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277Protein solution: 7-8 mg/ml protein in 30 mM Hepes, pH 7.5, 300 mM NaCl, 50 mM arginine/glutamine mix 1:1, 0.5 mM TCEP, and 1% v/v glycerol. Reservoir solution: 29% (v/v) 1,2 propanediol, 0.08 M Na/K phosphate. Crystals were soaked for 72 h in reservoir solution complemented with 1 mM compound and 20% ethylene glycol.
Crystal Properties
Matthews coefficientSolvent content
2.5551.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.791α = 90
b = 117.553β = 99
c = 91.911γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1347.11000.1620.9735.23.523961
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.181000.6120.6831.63.3

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-VALUE5v1j345.391.3423876118599.730.20050.19820.2439
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_d14.367
f_angle_d0.557
f_chiral_restr0.043
f_bond_d0.005
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7971
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms58

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing