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Crystal Structure of Adenine Phosphoribosyltransferase from Saccharomyces cerevisiae Complexed with D-2,5-Dideoxy-2,5-Imino-Altritol 1,6-Bisphosphate (D-DIAB) and Adenine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G2Q PDB entry 1G2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 100 mM sodium citrate, pH 5.6, 0.2 M ammonium sulfate, 25% PEG4000
Crystal Properties Matthews coefficient Solvent content 3.05 59.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.63 α = 90 b = 49.8 β = 131.04 c = 96.58 γ = 90
Symmetry Space Group C 1 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 MX-225HE 2017-02-09 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) R Merge I (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 1.78 72.85 97.9 0.11 0.99 6.9 3.3 46756 18.6
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 1.78 1.82 98.1 0.53 1.9 3.3
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 1G2Q 1.78 72.85 44449 2306 97.56 0.24678 0.24575 0.2533 0.26647 0.2755 RANDOM 22.474
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] 1.21 0.62 -1.45 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.252 r_dihedral_angle_4_deg 19.437 r_dihedral_angle_3_deg 12.563 r_dihedral_angle_1_deg 5.795 r_long_range_B_refined 4.883 r_long_range_B_other 4.875 r_mcangle_it 1.327 r_mcangle_other 1.327 r_angle_refined_deg 1.209 r_scangle_other 1.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.252 r_dihedral_angle_4_deg 19.437 r_dihedral_angle_3_deg 12.563 r_dihedral_angle_1_deg 5.795 r_long_range_B_refined 4.883 r_long_range_B_other 4.875 r_mcangle_it 1.327 r_mcangle_other 1.327 r_angle_refined_deg 1.209 r_scangle_other 1.203 r_angle_other_deg 0.884 r_mcbond_it 0.739 r_mcbond_other 0.738 r_scbond_it 0.69 r_scbond_other 0.69 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2668 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing