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Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 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, 5 mM MTA
Crystal Properties Matthews coefficient Solvent content 2.27757502 46.0287437
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.927 α = 90 b = 78.927 β = 90 c = 233.574 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 2024-06-24 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 1.69 44.4 100 0.088 0.098 0.043 0.999 18.9 10.1 31854
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 1.69 1.72 100 1.347 1.503 0.662 0.68 1.9 9.9
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 1.69 39.495 31849 1628 99.965 0.112 0.1097 0.1098 0.1439 0.1439 27.792
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] 0.059 0.03 0.059 -0.192
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.528 r_lrange_other 19.524 r_scangle_it 16.738 r_scangle_other 16.733 r_dihedral_angle_6_deg 15.198 r_dihedral_angle_3_deg 13.633 r_scbond_it 11.46 r_scbond_other 11.46 r_mcangle_it 10.318 r_mcangle_other 10.316
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.528 r_lrange_other 19.524 r_scangle_it 16.738 r_scangle_other 16.733 r_dihedral_angle_6_deg 15.198 r_dihedral_angle_3_deg 13.633 r_scbond_it 11.46 r_scbond_other 11.46 r_mcangle_it 10.318 r_mcangle_other 10.316 r_dihedral_angle_2_deg 9.053 r_mcbond_it 7.111 r_mcbond_other 7.108 r_dihedral_angle_1_deg 6.85 r_rigid_bond_restr 4.461 r_angle_refined_deg 1.824 r_angle_other_deg 0.621 r_nbd_refined 0.217 r_nbd_other 0.213 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.179 r_symmetry_nbd_refined 0.179 r_xyhbond_nbd_refined 0.127 r_symmetry_xyhbond_nbd_refined 0.12 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.084 r_dihedral_angle_other_2_deg 0.031 r_bond_refined_d 0.01 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 59 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction