6DDY

Crystal structure of the double mutant (D52N/K359Q) 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
1MICROBATCH7.52930.1 M HEPES (pH 7.5), 20% (w/v) PEG 1000, 0.1 M ammonium bromide, 5 mM ATP, 5 mM IMP, and 5 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
357

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.48α = 90
b = 126.84β = 90
c = 130.188γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2015-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL14-10.979SSRLBL14-1

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
11.80345.42599.40.0740.9844.113.36929435.1
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)
11.8031.861000.510.922.713.5

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-VALUE6DDH1.80345.4251.3469294700399.020.18680.1850.2031
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_d14.136
f_angle_d0.799
f_chiral_restr0.052
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3795
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms11

Software

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