6DWD

SAMHD1 Bound to Clofarabine-TP in the Catalytic Pocket and Allosteric Pocket


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH298100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.0339.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.477α = 90
b = 142.233β = 114.1
c = 98.79γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97920APS24-ID-C

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
11.75094.10.0860.999154.2209481
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7394.70.2834

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 DIFFRACTIONTHROUGHOUT1.7501988531058993.980.177520.176230.20155RANDOM28.521
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]
0.560.05-0.32-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.273
r_dihedral_angle_3_deg15.961
r_dihedral_angle_4_deg15.088
r_long_range_B_refined8.242
r_long_range_B_other8.242
r_scangle_other5.866
r_dihedral_angle_1_deg5.667
r_mcangle_it4.161
r_mcangle_other4.161
r_scbond_it3.803
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.273
r_dihedral_angle_3_deg15.961
r_dihedral_angle_4_deg15.088
r_long_range_B_refined8.242
r_long_range_B_other8.242
r_scangle_other5.866
r_dihedral_angle_1_deg5.667
r_mcangle_it4.161
r_mcangle_other4.161
r_scbond_it3.803
r_scbond_other3.8
r_mcbond_it2.818
r_mcbond_other2.817
r_angle_refined_deg2.133
r_angle_other_deg1.131
r_chiral_restr0.132
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms15609
Nucleic Acid Atoms
Solvent Atoms1050
Heterogen Atoms489

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing