6DW5

SAMHD1 Bound to Gemcitabine-TP in the Catalytic 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
2.0540.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.686α = 90
b = 142.901β = 113.92
c = 98.907γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97910APS24-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
11.9350970.0930.99813.23.5148608
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)
11.931.9696.40.7750.5213.3

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 DIFFRACTIONTHROUGHOUT1.9390.41141136743496.990.174870.173280.20536RANDOM36.856
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]
0.770.10.08-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.019
r_dihedral_angle_3_deg16.965
r_dihedral_angle_4_deg16.325
r_long_range_B_refined7.047
r_long_range_B_other7.04
r_dihedral_angle_1_deg5.715
r_scangle_other3.943
r_mcangle_it2.732
r_mcangle_other2.732
r_scbond_other2.492
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.019
r_dihedral_angle_3_deg16.965
r_dihedral_angle_4_deg16.325
r_long_range_B_refined7.047
r_long_range_B_other7.04
r_dihedral_angle_1_deg5.715
r_scangle_other3.943
r_mcangle_it2.732
r_mcangle_other2.732
r_scbond_other2.492
r_scbond_it2.491
r_angle_refined_deg2.254
r_mcbond_it1.709
r_mcbond_other1.709
r_angle_other_deg1.15
r_chiral_restr0.14
r_bond_refined_d0.022
r_gen_planes_refined0.011
r_bond_other_d0.003
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 Atoms15616
Nucleic Acid Atoms
Solvent Atoms597
Heterogen Atoms383

Software

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