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Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 343K
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 293.2 he 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 2.27136 45.8812599
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.854 α = 90 b = 78.854 β = 90 c = 233.369 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 343 PIXEL DECTRIS EIGER X 16M 2024-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 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 1.65 44.36 100 0.141 0.157 0.068 0.997 10 10 34102
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) 1.65 1.68 100 2.469 2.752 1.203 0.339 1.1 10
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 1.65 44.36 34101 1788 99.953 0.121 0.1182 0.1179 0.1674 0.1668 28.908
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] -0.329 -0.165 -0.329 1.067
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.605 r_lrange_other 19.601 r_scangle_it 16.426 r_scangle_other 16.421 r_dihedral_angle_6_deg 15.782 r_dihedral_angle_3_deg 13.072 r_scbond_it 11.042 r_scbond_other 11.041 r_mcangle_it 10.245 r_mcangle_other 10.242
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.605 r_lrange_other 19.601 r_scangle_it 16.426 r_scangle_other 16.421 r_dihedral_angle_6_deg 15.782 r_dihedral_angle_3_deg 13.072 r_scbond_it 11.042 r_scbond_other 11.041 r_mcangle_it 10.245 r_mcangle_other 10.242 r_dihedral_angle_1_deg 6.961 r_dihedral_angle_2_deg 6.961 r_mcbond_it 6.832 r_mcbond_other 6.822 r_rigid_bond_restr 4.03 r_angle_refined_deg 1.668 r_angle_other_deg 0.58 r_symmetry_nbd_refined 0.3 r_nbd_refined 0.215 r_nbd_other 0.21 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_refined 0.058 r_dihedral_angle_other_2_deg 0.057 r_bond_refined_d 0.009 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 55 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction