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Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 343K 1.58 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 5.4 293.2 The mixture of protein solution and agarose was 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 2.27741838 46.025032
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.94 α = 90 b = 78.94 β = 90 c = 233.481 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 343 PIXEL DECTRIS EIGER X 16M 2024-11-24 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 1.58 44.39 99.9 0.058 0.065 0.028 1 25.7 10 38817
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) 1.58 1.61 100 1.047 1.166 0.509 0.669 2.4 10.2
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 1.58 44.39 38816 1944 99.912 0.142 0.1412 0.1534 0.1628 0.1696 27.383
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] 0.205 0.103 0.205 -0.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.893 r_dihedral_angle_3_deg 13.456 r_dihedral_angle_2_deg 9.857 r_lrange_other 9.835 r_lrange_it 9.83 r_scangle_it 7.996 r_scangle_other 7.994 r_dihedral_angle_1_deg 6.999 r_scbond_it 5.21 r_scbond_other 5.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.893 r_dihedral_angle_3_deg 13.456 r_dihedral_angle_2_deg 9.857 r_lrange_other 9.835 r_lrange_it 9.83 r_scangle_it 7.996 r_scangle_other 7.994 r_dihedral_angle_1_deg 6.999 r_scbond_it 5.21 r_scbond_other 5.208 r_mcangle_it 3.785 r_mcangle_other 3.784 r_mcbond_it 2.602 r_mcbond_other 2.602 r_angle_refined_deg 1.981 r_angle_other_deg 0.651 r_symmetry_nbd_refined 0.242 r_nbd_refined 0.218 r_nbd_other 0.201 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.141 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.087 r_xyhbond_nbd_other 0.054 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_dihedral_angle_other_2_deg 0.006 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 48 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction