6YOM

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


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, 15% (w/v) PEG 3350, 0.05 M MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.2545.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.298α = 90
b = 105.298β = 90
c = 195.629γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I031.9075DiamondI03

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
13.25195.631000.2040.2110.0530.99710.515.41809486.2
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)
13.253.3199.441.3361.3810.3490.7522.115.4

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 REPLACEMENTTHROUGHOUT6TX03.2592.721710093199.920.17890.17590.2359RANDOM76.14
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]
-0.13-0.130.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.855
r_dihedral_angle_3_deg15.548
r_dihedral_angle_4_deg15.507
r_dihedral_angle_1_deg6.856
r_angle_refined_deg1.846
r_angle_other_deg1.083
r_chiral_restr0.097
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.855
r_dihedral_angle_3_deg15.548
r_dihedral_angle_4_deg15.507
r_dihedral_angle_1_deg6.856
r_angle_refined_deg1.846
r_angle_other_deg1.083
r_chiral_restr0.097
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7210
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms188

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction