6DZ3

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-(((3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl)thio)methyl)pyrrolidin-3-ol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TC6PDB entry 5TC6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6295100 mM sodium acetate trihydrate, pH 4.6, 2.0 M sodium chloride
Crystal Properties
Matthews coefficientSolvent content
2.242.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.355α = 90
b = 135.133β = 90
c = 158.86γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEKB mirrors2017-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.9179.4399.90.99137.566387
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.911.950.71.9

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 REPLACEMENTTHROUGHOUTPDB entry 5TC61.9179.4362924341699.90.198380.197130.22048RANDOM37.196
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]
-1.180.121.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.21
r_dihedral_angle_4_deg14.892
r_dihedral_angle_3_deg13.694
r_long_range_B_refined6.363
r_long_range_B_other6.362
r_dihedral_angle_1_deg6.334
r_scangle_other3.963
r_mcangle_it3.755
r_mcangle_other3.754
r_scbond_it2.402
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.21
r_dihedral_angle_4_deg14.892
r_dihedral_angle_3_deg13.694
r_long_range_B_refined6.363
r_long_range_B_other6.362
r_dihedral_angle_1_deg6.334
r_scangle_other3.963
r_mcangle_it3.755
r_mcangle_other3.754
r_scbond_it2.402
r_scbond_other2.402
r_mcbond_it2.292
r_mcbond_other2.292
r_angle_refined_deg1.479
r_angle_other_deg0.93
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms6256
Nucleic Acid Atoms
Solvent Atoms338
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing