4BZB

Crystal structure of the tetrameric dGTP-bound SAMHD1 mutant catalytic core


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3U1NPDB ENTRY 3U1N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.4100 MM SPG BUFFER, PH 7.4, 25% PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.203α = 90
b = 146.746β = 114.42
c = 98.723γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25

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
11.83501000.114.86.4197125129.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.831.8610015.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3U1N1.8348.73187162992399.670.18960.188710.20612RANDOM39.66
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]
1.240.64-1.33-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.339
r_dihedral_angle_3_deg15.155
r_dihedral_angle_4_deg14.865
r_dihedral_angle_1_deg4.574
r_mcangle_it1.79
r_angle_refined_deg1.112
r_mcbond_it1.036
r_mcbond_other1.035
r_scbond_it1.033
r_angle_other_deg0.728
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.339
r_dihedral_angle_3_deg15.155
r_dihedral_angle_4_deg14.865
r_dihedral_angle_1_deg4.574
r_mcangle_it1.79
r_angle_refined_deg1.112
r_mcbond_it1.036
r_mcbond_other1.035
r_scbond_it1.033
r_angle_other_deg0.728
r_chiral_restr0.061
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15732
Nucleic Acid Atoms
Solvent Atoms877
Heterogen Atoms380

Software

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