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Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 333K
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 2.27440357 45.9534874
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.924 α = 90 b = 78.924 β = 90 c = 233.512 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 333 PIXEL DECTRIS PILATUS3 S 6M 2024-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.98 Photon Factory BL-5A
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 1.61 44.39 100 0.071 0.079 0.034 0.999 23.7 10 36745
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.64 100 1.029 0.496 0.672 2.6 10.1
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 1.61 44.39 36744 1847 99.967 0.141 0.1398 0.1513 0.1683 0.1742 27.114
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] 0.14 0.07 0.14 -0.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.136 r_dihedral_angle_3_deg 13.686 r_lrange_it 9.911 r_lrange_other 9.911 r_dihedral_angle_2_deg 9.445 r_scangle_it 8.045 r_scangle_other 8.043 r_dihedral_angle_1_deg 6.846 r_scbond_it 5.125 r_scbond_other 5.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.136 r_dihedral_angle_3_deg 13.686 r_lrange_it 9.911 r_lrange_other 9.911 r_dihedral_angle_2_deg 9.445 r_scangle_it 8.045 r_scangle_other 8.043 r_dihedral_angle_1_deg 6.846 r_scbond_it 5.125 r_scbond_other 5.125 r_mcangle_it 4.528 r_mcangle_other 4.527 r_mcbond_it 3.026 r_mcbond_other 3.025 r_angle_refined_deg 1.993 r_angle_other_deg 0.66 r_nbd_refined 0.221 r_symmetry_nbd_other 0.201 r_nbd_other 0.188 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.1 r_symmetry_nbd_refined 0.1 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_refined 0.069 r_dihedral_angle_other_2_deg 0.047 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 54 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction