4TO2

Structure basis of cellular dNTP regulation, SAMHD1-dGTP-dGTP-dGTP/dTTP 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
2.3647.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.313α = 90
b = 145.798β = 114.22
c = 98.257γ = 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)R Sym 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
12.275099.90.1420.1428.94.999828
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)
12.282.3299.90.89314.84974

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 REPLACEMENTTHROUGHOUT4BZB2.275099162494198.310.20740.2060.2336RANDOM68.197
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]
-0.840.34-4.473.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.042
r_dihedral_angle_3_deg16.216
r_dihedral_angle_4_deg11.998
r_dihedral_angle_1_deg5.52
r_mcangle_it3.084
r_mcbond_it1.85
r_mcbond_other1.847
r_angle_refined_deg1.546
r_angle_other_deg1.056
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.042
r_dihedral_angle_3_deg16.216
r_dihedral_angle_4_deg11.998
r_dihedral_angle_1_deg5.52
r_mcangle_it3.084
r_mcbond_it1.85
r_mcbond_other1.847
r_angle_refined_deg1.546
r_angle_other_deg1.056
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15732
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms378

Software

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