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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-((pent-4-yn-1-ylthio)methyl)pyrrolidin-3-ol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TC6 PDB entry 5TC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 100 mM HEPES, pH 7.0, 10% w/v PEG6000
Crystal Properties Matthews coefficient Solvent content 2.9 57.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.812 α = 90 b = 121.812 β = 90 c = 44.372 γ = 120
Symmetry Space Group P 3 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE KB mirrors 2017-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.62 105.49 100 0.999 2 12.5 48221
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.65 0.714
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 5TC6 1.62 105.49 45734 2484 99.98 0.15641 0.15533 0.1675 0.17569 0.1873 RANDOM 22.645
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.819 r_dihedral_angle_4_deg 16.881 r_dihedral_angle_3_deg 11.554 r_long_range_B_refined 6.319 r_long_range_B_other 6.318 r_dihedral_angle_1_deg 6.199 r_scangle_other 3.814 r_scbond_it 2.45 r_scbond_other 2.449 r_mcangle_it 2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.819 r_dihedral_angle_4_deg 16.881 r_dihedral_angle_3_deg 11.554 r_long_range_B_refined 6.319 r_long_range_B_other 6.318 r_dihedral_angle_1_deg 6.199 r_scangle_other 3.814 r_scbond_it 2.45 r_scbond_other 2.449 r_mcangle_it 2.4 r_mcangle_other 2.4 r_angle_refined_deg 1.578 r_mcbond_it 1.496 r_mcbond_other 1.495 r_angle_other_deg 0.969 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 2113 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing