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Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 293K
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 2.27726746 46.0214539
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.97 α = 90 b = 78.97 β = 90 c = 233.288 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 293 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 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 1.62 44.38 100 0.1 0.112 0.049 0.999 16.7 9.9 36099
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) 1.62 1.65 100 1.218 1.36 0.599 0.697 2.2 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 1.62 44.38 36097 1871 99.972 0.146 0.1449 0.1586 0.1711 0.1815 22.513
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] -0.08 -0.04 -0.08 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.265 r_dihedral_angle_3_deg 12.606 r_dihedral_angle_2_deg 7.852 r_lrange_it 7.565 r_lrange_other 7.552 r_dihedral_angle_1_deg 6.731 r_scangle_it 6.506 r_scangle_other 6.504 r_scbond_it 4.177 r_scbond_other 4.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.265 r_dihedral_angle_3_deg 12.606 r_dihedral_angle_2_deg 7.852 r_lrange_it 7.565 r_lrange_other 7.552 r_dihedral_angle_1_deg 6.731 r_scangle_it 6.506 r_scangle_other 6.504 r_scbond_it 4.177 r_scbond_other 4.177 r_mcangle_it 2.742 r_mcangle_other 2.741 r_mcbond_it 1.932 r_mcbond_other 1.93 r_angle_refined_deg 1.831 r_angle_other_deg 0.627 r_nbd_refined 0.211 r_symmetry_nbd_other 0.193 r_nbd_other 0.181 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.156 r_xyhbond_nbd_refined 0.132 r_symmetry_xyhbond_nbd_refined 0.117 r_chiral_restr 0.094 r_dihedral_angle_other_2_deg 0.083 r_symmetry_nbtor_other 0.083 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 88 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction