X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8JBKdeposition ID: D_1300037566

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2283285 mM NaCl, 25 mM MgCl2, 15.4% (w/v) PEG2000MME, 7% (w/v) glycerol, 5 mM GSH, 0.1 mM DTT and 1 mg/ml butylhydroxytoluen, 100 mM MES
Crystal Properties
Matthews coefficientSolvent content
3.4664.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 196.797α = 90
b = 74.319β = 116.289
c = 163.553γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1SPring-8BL41XU

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
133053.70.1740.9737.033.54600082.69
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)
133.14.10.6030.2831.341.6

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-VALUE8JBK311.991.3644648224353.050.23560.2330.282390.02
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_d17.8208
f_angle_d0.7767
f_chiral_restr0.047
f_plane_restr0.0054
f_bond_d0.0038
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20765
Nucleic Acid Atoms
Solvent Atoms33
Heterogen Atoms884

Software

Software
Software NamePurpose
BSSdata collection
HKL-2000data reduction
STARANISOdata scaling
PHASERphasing
PHENIXrefinement