4BZC

Crystal structure of the tetrameric dGTP-bound wild type SAMHD1 catalytic core


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.7100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.002α = 90
b = 138.727β = 113.56
c = 93.715γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-CAPS24-ID-C

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
12.885095.60.128.22.9403691
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.882.9397.40.91.23

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 3U1N2.8849.7131009166877.510.193070.190320.2448RANDOM66.501
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]
0.120.7-1.991.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.288
r_dihedral_angle_3_deg17.639
r_dihedral_angle_4_deg14.698
r_dihedral_angle_1_deg5.316
r_mcangle_it4.462
r_scbond_it3.011
r_mcbond_it2.721
r_mcbond_other2.719
r_angle_refined_deg1.673
r_angle_other_deg1.289
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.288
r_dihedral_angle_3_deg17.639
r_dihedral_angle_4_deg14.698
r_dihedral_angle_1_deg5.316
r_mcangle_it4.462
r_scbond_it3.011
r_mcbond_it2.721
r_mcbond_other2.719
r_angle_refined_deg1.673
r_angle_other_deg1.289
r_chiral_restr0.098
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.006
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 Atoms15540
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms380

Software

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