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Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 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 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 2.28176999 46.1279678
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.044 α = 90 b = 79.044 β = 90 c = 233.312 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 2024-11-24 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 1.7 44.4 100 0.095 0.105 0.046 0.999 20.8 10 31368
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 1.7 1.73 100 1.179 1.288 0.572 0.676 2.5 9.8
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 1.7 44.4 31367 1611 99.971 0.147 0.1452 0.1572 0.1819 0.1886 27.831
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] 0.141 0.07 0.141 -0.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.221 r_dihedral_angle_3_deg 13.949 r_lrange_other 10.346 r_lrange_it 10.343 r_scangle_it 8.237 r_scangle_other 8.234 r_dihedral_angle_1_deg 7.342 r_dihedral_angle_2_deg 6.727 r_scbond_it 5.161 r_scbond_other 5.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.221 r_dihedral_angle_3_deg 13.949 r_lrange_other 10.346 r_lrange_it 10.343 r_scangle_it 8.237 r_scangle_other 8.234 r_dihedral_angle_1_deg 7.342 r_dihedral_angle_2_deg 6.727 r_scbond_it 5.161 r_scbond_other 5.161 r_mcangle_it 4.065 r_mcangle_other 4.064 r_mcbond_it 2.784 r_mcbond_other 2.784 r_angle_refined_deg 1.831 r_angle_other_deg 0.606 r_symmetry_nbd_refined 0.309 r_nbd_other 0.223 r_nbd_refined 0.22 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.087 r_dihedral_angle_other_2_deg 0.07 r_symmetry_xyhbond_nbd_refined 0.061 r_bond_refined_d 0.01 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 45 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction