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Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 293K
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 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.10%(v/v)PEG#200,0.1 M
phosphate citrate pH 5.4, 2.5 mM MTA
Crystal Properties Matthews coefficient Solvent content 2.27516794 45.9716454
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.876 α = 90 b = 78.876 β = 90 c = 233.629 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 293 PIXEL DECTRIS EIGER X 16M 2024-02-10 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 1.39 44.39 100 0.056 0.062 0.027 0.999 19.9 10 56723
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 1.39 1.41 100 1.137 1.269 0.556 0.685 2.2 9.7
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 1.39 44.39 56722 2773 99.982 0.118 0.1169 0.1162 0.1431 0.142 23.32
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] -0.092 -0.046 -0.092 0.299
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.609 r_lrange_other 19.605 r_dihedral_angle_6_deg 15.771 r_scangle_it 15.613 r_scangle_other 15.609 r_dihedral_angle_3_deg 12.204 r_mcangle_it 11.473 r_mcangle_other 11.469 r_scbond_it 10.936 r_scbond_other 10.935
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.609 r_lrange_other 19.605 r_dihedral_angle_6_deg 15.771 r_scangle_it 15.613 r_scangle_other 15.609 r_dihedral_angle_3_deg 12.204 r_mcangle_it 11.473 r_mcangle_other 11.469 r_scbond_it 10.936 r_scbond_other 10.935 r_dihedral_angle_2_deg 9.892 r_mcbond_it 8.293 r_mcbond_other 8.283 r_dihedral_angle_1_deg 7.142 r_rigid_bond_restr 4.837 r_angle_refined_deg 1.992 r_angle_other_deg 0.688 r_symmetry_nbd_refined 0.296 r_nbd_refined 0.242 r_nbd_other 0.235 r_symmetry_nbd_other 0.211 r_nbtor_refined 0.183 r_dihedral_angle_other_2_deg 0.157 r_symmetry_xyhbond_nbd_refined 0.146 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.012 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 2153 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction