X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5V2T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8277.150.5 ul 72 mg/ml EFE (25 mM HEPES pH 8.0, 1 mM TCEP) was mixed with 0.5 ul reservoir solution. The sitting drop reservoir of 200 ul contained 0.2 M lithium chloride, 0.1 M Tris-HCl pH 8.0, 20% w/v Polyethylene glycol 6,000. A grown crystal was soaked for 2 hours in a sitting drop containing 0.1 M nickel chloride, 0.2 M lithium chloride, 0.1 M Tris-HCl pH 8.0, 20% w/v Polyethylene glycol 6,000, the reservoir of 100 ul contained 0.2 M lithium chloride, 0.1 M Tris-HCl pH 8.0, 20% w/v Polyethylene glycol 6,000.The crystal was direcly frozen.
Crystal Properties
Matthews coefficientSolvent content
1.8132.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.79α = 90
b = 79.31β = 90
c = 87.75γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2016-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.4777APS21-ID-D

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
13.0487.7599.30.1410.1570.0690.9974.8595954.66
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)
13.043.2299.70.3820.4240.1810.9415.1941

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-VALUE5V2T3.0443.8751.93530884797.960.20860.19880.267547.67
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_d2.665
f_angle_d0.533
f_chiral_restr0.039
f_bond_d0.005
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2316
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms1

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction