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Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 353K
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
Crystal Properties Matthews coefficient Solvent content 2.286 46.228
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.127 α = 90 b = 79.127 β = 90 c = 233.26 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 2024-10-27 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 1.68 44.41 100 0.068 0.076 0.033 0.999 21.6 10 32535
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 1.68 1.71 100 0.999 1.115 0.49 0.692 2.7 9.9
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 (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 1.68 44.41 32533 1596 99.923 0.141 0.14 0.1511 0.1687 0.1738 28.816
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] 0.102 0.051 0.102 -0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.6 r_dihedral_angle_3_deg 13.942 r_lrange_it 10.341 r_lrange_other 10.34 r_dihedral_angle_2_deg 8.858 r_scangle_it 8.335 r_scangle_other 8.332 r_dihedral_angle_1_deg 6.877 r_scbond_it 5.267 r_scbond_other 5.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.6 r_dihedral_angle_3_deg 13.942 r_lrange_it 10.341 r_lrange_other 10.34 r_dihedral_angle_2_deg 8.858 r_scangle_it 8.335 r_scangle_other 8.332 r_dihedral_angle_1_deg 6.877 r_scbond_it 5.267 r_scbond_other 5.266 r_mcangle_it 3.975 r_mcangle_other 3.973 r_mcbond_it 2.824 r_mcbond_other 2.824 r_angle_refined_deg 1.892 r_angle_other_deg 0.638 r_nbd_refined 0.215 r_nbd_other 0.202 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.179 r_symmetry_nbd_refined 0.157 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.096 r_symmetry_xyhbond_nbd_refined 0.09 r_symmetry_nbtor_other 0.085 r_dihedral_angle_other_2_deg 0.043 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 48 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction