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Intermediate state structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix at high temperature (363K) after 10 minutes reaction 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, 5mM MTA
Crystal Properties Matthews coefficient Solvent content 2.28471565 46.1974258
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.042 α = 90 b = 79.042 β = 90 c = 233.625 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 363 PIXEL DECTRIS EIGER X 16M 2025-07-02 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 2.08 44.43 100 0.194 0.215 0.092 0.997 13.2 10.2 17322
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) 2.08 2.14 100 1.123 1.242 0.526 0.674 2.6 10.7
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 2.08 44.43 17322 894 99.954 0.145 0.1439 0.156 0.1741 0.182 32.015
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] 0.285 0.143 0.285 -0.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.854 r_dihedral_angle_6_deg 14.683 r_lrange_it 10.455 r_lrange_other 10.454 r_dihedral_angle_2_deg 8.18 r_scangle_it 8.084 r_scangle_other 8.081 r_dihedral_angle_1_deg 7.416 r_scbond_it 4.967 r_scbond_other 4.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.854 r_dihedral_angle_6_deg 14.683 r_lrange_it 10.455 r_lrange_other 10.454 r_dihedral_angle_2_deg 8.18 r_scangle_it 8.084 r_scangle_other 8.081 r_dihedral_angle_1_deg 7.416 r_scbond_it 4.967 r_scbond_other 4.966 r_mcangle_it 4.386 r_mcangle_other 4.384 r_mcbond_it 2.824 r_mcbond_other 2.821 r_angle_refined_deg 1.746 r_angle_other_deg 0.564 r_nbd_refined 0.213 r_symmetry_nbd_other 0.196 r_nbd_other 0.187 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.129 r_symmetry_xyhbond_nbd_refined 0.118 r_symmetry_nbd_refined 0.092 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.081 r_dihedral_angle_other_2_deg 0.055 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 30 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction