6DDH

Crystal structure of the double mutant (D52N/R367Q) 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 2XCW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.52930.1 M HEPES (pH 7.5), 20% (w/v) PEG 1000, and 0.1 M ammonium nitrate, 5 mM ATP, 5 mM IMP, 5 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
358

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.916α = 90
b = 127.762β = 90
c = 130.305γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2014-08-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.979NSLSX4C

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
12.3548.6611000.090.10.040.98287.43259337.7
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)
12.352.3999.90.480.520.20.9846.8

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 REPLACEMENTTHROUGHOUT2XCW2.3548.6611.3432292323599.910.18590.18170.2229
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_d13.858
f_angle_d0.834
f_chiral_restr0.051
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3851
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms23

Software

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