☰ Navigation Tabs
Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 353K 1.77 angstrom
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. 15%(v/v)PEG#200, 0.1M phosphate citrate pH5.4, 5mM MTA.
Crystal Properties Matthews coefficient Solvent content 2.28364396 46.1721764
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.048 α = 90 b = 79.048 β = 90 c = 233.48 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 2024-06-02 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 1.77 39.52 100 0.112 0.124 0.054 0.999 12.7 9.9 27838
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) 1.77 1.81 100 1.253 1.416 0.652 0.691 2.5 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 1.77 38.944 27837 1399 99.939 0.142 0.1406 0.1535 0.1754 0.1801 30.513
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] 0.3 0.15 0.3 -0.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.255 r_dihedral_angle_3_deg 13.609 r_lrange_other 10.885 r_lrange_it 10.884 r_dihedral_angle_2_deg 8.641 r_scangle_it 8.544 r_scangle_other 8.542 r_dihedral_angle_1_deg 7.054 r_scbond_it 5.334 r_scbond_other 5.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.255 r_dihedral_angle_3_deg 13.609 r_lrange_other 10.885 r_lrange_it 10.884 r_dihedral_angle_2_deg 8.641 r_scangle_it 8.544 r_scangle_other 8.542 r_dihedral_angle_1_deg 7.054 r_scbond_it 5.334 r_scbond_other 5.334 r_mcangle_it 4.363 r_mcangle_other 4.362 r_mcbond_it 2.977 r_mcbond_other 2.977 r_angle_refined_deg 1.835 r_angle_other_deg 0.623 r_nbd_refined 0.213 r_nbd_other 0.206 r_symmetry_nbd_refined 0.201 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.129 r_symmetry_xyhbond_nbd_refined 0.105 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.085 r_dihedral_angle_other_2_deg 0.019 r_gen_planes_refined 0.011 r_bond_refined_d 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 25
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction