☰ Navigation Tabs
High temperature (363K) crystal structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix after 30 minutes reaction with substrate
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, methylcellurose 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 pH 5.4, 5mM MTA
Crystal Properties Matthews coefficient Solvent content 2.27571559 45.9846382
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.997 α = 90 b = 78.997 β = 90 c = 232.969 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 363 PIXEL DECTRIS EIGER X 16M 2025-07-02 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 1.79 44.35 99.9 0.224 0.252 0.112 0.985 12.4 9.6 26844
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) 1.79 1.83 100 1.22 1.368 0.614 0.704 3.2 9.5
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 1.79 44.35 26842 1391 99.903 0.151 0.1494 0.1593 0.1759 0.1864 28.444
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] 0.021 0.01 0.021 -0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.826 r_dihedral_angle_3_deg 14.104 r_lrange_it 10.159 r_lrange_other 10.159 r_dihedral_angle_2_deg 8.531 r_scangle_it 7.712 r_scangle_other 7.71 r_dihedral_angle_1_deg 6.939 r_scbond_it 4.885 r_scbond_other 4.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.826 r_dihedral_angle_3_deg 14.104 r_lrange_it 10.159 r_lrange_other 10.159 r_dihedral_angle_2_deg 8.531 r_scangle_it 7.712 r_scangle_other 7.71 r_dihedral_angle_1_deg 6.939 r_scbond_it 4.885 r_scbond_other 4.884 r_mcangle_it 4.184 r_mcangle_other 4.183 r_mcbond_it 2.789 r_mcbond_other 2.788 r_angle_refined_deg 1.852 r_angle_other_deg 0.62 r_nbd_refined 0.21 r_symmetry_nbd_refined 0.208 r_nbd_other 0.204 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.14 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.086 r_dihedral_angle_other_2_deg 0.054 r_symmetry_xyhbond_nbd_other 0.051 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 2140 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction