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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-(((3-(1-benzyl-1H-1,2,3-triazol-4-yl)propyl)thio)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 4.6 295 100 mM sodium acetate trihydrate, pH 4.6, 2.0 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.2 42.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.39 α = 90 b = 135.316 β = 90 c = 159.268 γ = 90
Symmetry Space Group C 2 2 21
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 2017-12-12 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 1.99 79.63 99.9 0.99 13.4 7.4 59017
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 1.99 2.04 0.73 1.9
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 1.99 79.63 56168 2807 99.88 0.20294 0.20125 0.2099 0.23575 0.2397 RANDOM 42.593
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] -2.03 -1.57 3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.226 r_dihedral_angle_4_deg 15.77 r_dihedral_angle_3_deg 14.239 r_long_range_B_refined 7.639 r_long_range_B_other 7.638 r_dihedral_angle_1_deg 6.192 r_scangle_other 5.35 r_mcangle_it 4.527 r_mcangle_other 4.526 r_scbond_it 3.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.226 r_dihedral_angle_4_deg 15.77 r_dihedral_angle_3_deg 14.239 r_long_range_B_refined 7.639 r_long_range_B_other 7.638 r_dihedral_angle_1_deg 6.192 r_scangle_other 5.35 r_mcangle_it 4.527 r_mcangle_other 4.526 r_scbond_it 3.355 r_scbond_other 3.355 r_mcbond_it 2.889 r_mcbond_other 2.889 r_angle_refined_deg 1.516 r_angle_other_deg 0.931 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 6164 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing