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Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 5.4 293.2 The mixture of protein solution and agarose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition of the reservoir solution was as follows.15%(v/v)PEG#200,0.1 M phosphate citrate pH 5.4, 5 mM MTA
Crystal Properties Matthews coefficient Solvent content 2.16 43.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.646 α = 90 b = 77.646 β = 90 c = 230.39 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2024-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.22 43.74 100 0.107 0.12 0.053 0.999 13.2 10 79813
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.22 1.24 2.221 2.48 1.092 0.382 10
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1WTA 1.22 38.853 79810 4025 99.98 0.143 0.1422 0.1424 0.166 0.1644 15.772
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] 0.006 0.003 0.006 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.06 r_dihedral_angle_3_deg 12.682 r_lrange_it 11.891 r_lrange_other 11.89 r_dihedral_angle_2_deg 10.009 r_scangle_it 8.795 r_scangle_other 8.792 r_dihedral_angle_1_deg 6.92 r_scbond_other 6.353 r_scbond_it 6.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.06 r_dihedral_angle_3_deg 12.682 r_lrange_it 11.891 r_lrange_other 11.89 r_dihedral_angle_2_deg 10.009 r_scangle_it 8.795 r_scangle_other 8.792 r_dihedral_angle_1_deg 6.92 r_scbond_other 6.353 r_scbond_it 6.352 r_mcangle_it 5.739 r_mcangle_other 5.737 r_mcbond_it 3.987 r_mcbond_other 3.983 r_rigid_bond_restr 3.908 r_angle_refined_deg 1.93 r_angle_other_deg 0.665 r_nbd_refined 0.224 r_nbd_other 0.209 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.162 r_dihedral_angle_other_2_deg 0.153 r_symmetry_xyhbond_nbd_refined 0.136 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.084 r_xyhbond_nbd_other 0.064 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2142 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction