5LF8

Human Nucleoside diphosphate-linked moiety X motif 17 (NUDT17)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72770.1 M SPG pH 7.0 30% PEG1K
Crystal Properties
Matthews coefficientSolvent content
2.5251.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.913α = 90
b = 151.913β = 90
c = 81.495γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9900DiamondI02

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
12.5675.961000.0671810.211806
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.56

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 DIFFRACTIONSADTHROUGHOUT2.5675.961118362199.970.230720.22720.29823RANDOM69.608
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]
-3.26-1.63-3.2610.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.852
r_dihedral_angle_3_deg15.32
r_dihedral_angle_4_deg15.109
r_long_range_B_refined11.343
r_long_range_B_other11.34
r_mcangle_it8.54
r_mcangle_other8.538
r_dihedral_angle_1_deg8.056
r_scangle_other7.964
r_mcbond_other5.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.852
r_dihedral_angle_3_deg15.32
r_dihedral_angle_4_deg15.109
r_long_range_B_refined11.343
r_long_range_B_other11.34
r_mcangle_it8.54
r_mcangle_other8.538
r_dihedral_angle_1_deg8.056
r_scangle_other7.964
r_mcbond_other5.8
r_mcbond_it5.799
r_scbond_it5.451
r_scbond_other5.429
r_angle_refined_deg1.617
r_angle_other_deg0.989
r_chiral_restr0.081
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1770
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
autoSHARPphasing