6DYZ

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-((prop-2-yn-1-ylthio)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 DROP7295100 mM HEPES, pH 7.0, 10% w/v PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.958.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.821α = 90
b = 122.821β = 90
c = 44.624γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEKB mirrors2017-11-14MSINGLE 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
11.62106.3798.60.999212.548526
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)
11.621.650.758

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 5TC61.62106.3746245226898.370.170390.169430.18999RANDOM22.065
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]
-0.49-0.25-0.491.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.854
r_dihedral_angle_4_deg14.656
r_dihedral_angle_3_deg12.214
r_dihedral_angle_1_deg6.302
r_long_range_B_refined5.589
r_long_range_B_other5.588
r_scangle_other3.56
r_mcangle_it2.279
r_mcangle_other2.279
r_scbond_it2.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.854
r_dihedral_angle_4_deg14.656
r_dihedral_angle_3_deg12.214
r_dihedral_angle_1_deg6.302
r_long_range_B_refined5.589
r_long_range_B_other5.588
r_scangle_other3.56
r_mcangle_it2.279
r_mcangle_other2.279
r_scbond_it2.209
r_scbond_other2.208
r_angle_refined_deg1.573
r_mcbond_it1.424
r_mcbond_other1.418
r_angle_other_deg0.941
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2112
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing