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High temperature (353K) crystal structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix with substrate
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, methylcellulose 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, 0.1M phosphate citrate pH5.4, 5 mM MTA
Crystal Properties Matthews coefficient Solvent content 2.28788519 46.2719612
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.076 α = 90 b = 79.076 β = 90 c = 233.748 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 353 PIXEL DECTRIS EIGER X 16M 2025-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 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 1.83 44.45 100 0.145 0.161 0.069 0.997 10.7 10.1 25314
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) 1.83 1.87 100 1.066 1.19 0.525 0.705 2.9 9.8
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 1.83 44.45 25313 1262 99.968 0.142 0.1402 0.1522 0.1678 0.1747 28.902
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] 0.155 0.077 0.155 -0.503
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.985 r_dihedral_angle_3_deg 14.078 r_lrange_other 9.967 r_lrange_it 9.964 r_dihedral_angle_2_deg 8.093 r_scangle_other 8.081 r_scangle_it 8.075 r_dihedral_angle_1_deg 7.274 r_scbond_other 5.052 r_scbond_it 5.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.985 r_dihedral_angle_3_deg 14.078 r_lrange_other 9.967 r_lrange_it 9.964 r_dihedral_angle_2_deg 8.093 r_scangle_other 8.081 r_scangle_it 8.075 r_dihedral_angle_1_deg 7.274 r_scbond_other 5.052 r_scbond_it 5.049 r_mcangle_it 3.981 r_mcangle_other 3.979 r_mcbond_it 2.764 r_mcbond_other 2.764 r_angle_refined_deg 1.805 r_angle_other_deg 0.606 r_nbd_refined 0.215 r_symmetry_nbd_other 0.196 r_nbd_other 0.185 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.137 r_symmetry_nbd_refined 0.117 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.085 r_dihedral_angle_other_2_deg 0.022 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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 38 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction