5WTU

Crystal structure of DndE G21/24K mutant involved in DNA phosphorothioation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6291.150.1 M Sodium citrate tribasic dihydrate pH 5.6, 0.2 M Potassium sodium tartrate tetrahydrate, 2.0 M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.1141.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.297α = 90
b = 57.297β = 90
c = 130.222γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97915SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.95097.60.1356.33.59087
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.9399.20.5163.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2.950.01862343297.610.22730.22520.272RANDOM42.31
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]
0.610.61-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.874
r_sphericity_bonded26.971
r_dihedral_angle_3_deg17.985
r_dihedral_angle_4_deg14.918
r_dihedral_angle_1_deg4.828
r_rigid_bond_restr2.406
r_angle_refined_deg1.196
r_chiral_restr0.07
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3114
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
HKLdata scaling