6TXF

Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dAMPNPP and Mn


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6TX0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.1 M Bistris methane-HCl pH 6, 14% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2445.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.978α = 90
b = 104.978β = 90
c = 195.516γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.97866DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.2571.5997.750.1220.1260.0290.99814.516.835160337.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.2980.131.2161.3070.4630.6731.86.84

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 REPLACEMENTTHROUGHOUT6TX02.2571.5148696256897.420.19740.19520.2388RANDOM47.142
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]
0.170.17-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.701
r_dihedral_angle_4_deg16.929
r_dihedral_angle_3_deg15.242
r_dihedral_angle_1_deg5.942
r_angle_refined_deg2.095
r_angle_other_deg1.14
r_chiral_restr0.122
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.701
r_dihedral_angle_4_deg16.929
r_dihedral_angle_3_deg15.242
r_dihedral_angle_1_deg5.942
r_angle_refined_deg2.095
r_angle_other_deg1.14
r_chiral_restr0.122
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7748
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms192

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction