4TO6

Structure basis of cellular dNTP regulation, SAMHD1-dGTP-dATP-dTTP/dGTP complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BZB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE298SPG buffer, PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.1643.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.587α = 90
b = 140.808β = 114.94
c = 96.9γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.9792APS24-ID-E

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
12.33501000.1557.38.985312
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.391007.94276

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 REPLACEMENTTHROUGHOUT4BZB2.335085283425999.380.22570.22470.2439RANDOM72.955
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]
1.2-4.923.340.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.009
r_dihedral_angle_4_deg16.807
r_dihedral_angle_3_deg16.325
r_dihedral_angle_1_deg5.203
r_mcangle_it4.614
r_mcbond_it2.887
r_mcbond_other2.887
r_angle_refined_deg1.429
r_angle_other_deg0.93
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.009
r_dihedral_angle_4_deg16.807
r_dihedral_angle_3_deg16.325
r_dihedral_angle_1_deg5.203
r_mcangle_it4.614
r_mcbond_it2.887
r_mcbond_other2.887
r_angle_refined_deg1.429
r_angle_other_deg0.93
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.006
r_bond_other_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15700
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms366

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling