6TX0

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.1 M Bistris methane-HCl pH 6, 16% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3146.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.924α = 90
b = 105.924β = 90
c = 198.073γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-01-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

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
12.00672.34295.60.1130.120.0390.99914.39.34548336.1
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)
12.0062.25678.81.191.2640.4210.67428.9

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 REPLACEMENTTHROUGHOUT4bzc2.0172.3143168230660.150.18590.18360.2281RANDOM43.443
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]
-0.32-0.320.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.705
r_dihedral_angle_4_deg19.214
r_dihedral_angle_3_deg15.699
r_dihedral_angle_1_deg6.147
r_angle_refined_deg2.024
r_angle_other_deg1.119
r_chiral_restr0.115
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.705
r_dihedral_angle_4_deg19.214
r_dihedral_angle_3_deg15.699
r_dihedral_angle_1_deg6.147
r_angle_refined_deg2.024
r_angle_other_deg1.119
r_chiral_restr0.115
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7720
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms192

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
BUCCANEERmodel building
PDB_EXTRACTdata extraction