4RXR

The structure of GTP-dCTP-bound SAMHD1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MZ7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52950.1 M lithium sulfate monohydrate, 0.1M sodium citrate tribasic dihydrate, and 20% w/v polyethylene glycol 1000 , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5451.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.894α = 90
b = 108.26β = 122.92
c = 92.663γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.98SSRFBL17U

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
12.15099.60.07539.46.970499702171.51.543
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)
12.12.1499.10.5763.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4MZ72.11750116766266701350598.580.181190.179490.21347RANDOM49.707
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]
-2.110.381.360.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.097
r_dihedral_angle_4_deg15.252
r_dihedral_angle_3_deg14.86
r_long_range_B_refined6.928
r_long_range_B_other6.92
r_dihedral_angle_1_deg5.302
r_scangle_other5.141
r_mcangle_it3.761
r_mcangle_other3.76
r_scbond_it3.227
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.097
r_dihedral_angle_4_deg15.252
r_dihedral_angle_3_deg14.86
r_long_range_B_refined6.928
r_long_range_B_other6.92
r_dihedral_angle_1_deg5.302
r_scangle_other5.141
r_mcangle_it3.761
r_mcangle_other3.76
r_scbond_it3.227
r_scbond_other3.227
r_mcbond_it2.56
r_mcbond_other2.56
r_angle_other_deg2.381
r_angle_refined_deg1.34
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_gen_planes_other0.005
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7972
Nucleic Acid Atoms
Solvent Atoms426
Heterogen Atoms178

Software

Software
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling