6DDZ

Crystal structure of the double mutant (D52N/R238W) of NT5C2-537X in the active state, Northeast Structural Genomics Target


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6DDH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH729335% (w/v) tascimate (pH 7)
Crystal Properties
Matthews coefficientSolvent content
357

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.677α = 90
b = 127.293β = 90
c = 131.131γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-22015-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

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
11.9733.58399.80.0760.080.0230.9830.910.15441328.5
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)
11.972.051000.5880.6390.2440.882.96.6

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-VALUE6DDH1.9733.5831.3354414547598.890.18050.1780.2029
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_d15.502
f_angle_d0.844
f_chiral_restr0.052
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3856
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms50

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
COMOphasing