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Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 323K
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 2.28155518 46.1228981
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.065 α = 90 b = 79.065 β = 90 c = 233.167 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 323 PIXEL DECTRIS EIGER X 16M 2024-10-27 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 1.59 44.39 100 0.116 0.13 0.057 0.999 17.2 9.8 38232
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) 1.59 1.62 100 1.076 1.198 0.521 0.667 2.7 10.1
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 1.59 44.39 38229 1927 99.961 0.146 0.1448 0.157 0.1705 0.1799 23.324
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] 0.025 0.013 0.025 -0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.634 r_dihedral_angle_3_deg 14.631 r_lrange_other 10.188 r_lrange_it 10.187 r_dihedral_angle_2_deg 7.854 r_scangle_it 7.597 r_scangle_other 7.595 r_dihedral_angle_1_deg 6.935 r_scbond_it 4.886 r_scbond_other 4.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.634 r_dihedral_angle_3_deg 14.631 r_lrange_other 10.188 r_lrange_it 10.187 r_dihedral_angle_2_deg 7.854 r_scangle_it 7.597 r_scangle_other 7.595 r_dihedral_angle_1_deg 6.935 r_scbond_it 4.886 r_scbond_other 4.884 r_mcangle_it 3.477 r_mcangle_other 3.476 r_mcbond_it 2.307 r_mcbond_other 2.305 r_angle_refined_deg 1.927 r_angle_other_deg 0.662 r_nbd_refined 0.236 r_symmetry_nbd_other 0.203 r_nbd_other 0.198 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.177 r_symmetry_nbd_refined 0.15 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.07 r_dihedral_angle_other_2_deg 0.042 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 70 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction