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Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 333K
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 2.28063083 46.1010628
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.049 α = 90 b = 79.049 β = 90 c = 233.166 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 333 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 1.55 44.38 100 0.071 0.079 0.035 1 23.4 10 41175
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) 1.55 1.58 100 1.04 1.158 0.505 0.663 2.6 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 1.55 44.38 41173 2031 99.973 0.146 0.145 0.1572 0.1673 0.1808 23.554
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] 0.047 0.024 0.047 -0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.569 r_dihedral_angle_3_deg 13.197 r_lrange_it 8.626 r_lrange_other 8.624 r_dihedral_angle_2_deg 7.721 r_scangle_it 7.145 r_scangle_other 7.143 r_dihedral_angle_1_deg 6.839 r_scbond_it 4.63 r_scbond_other 4.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.569 r_dihedral_angle_3_deg 13.197 r_lrange_it 8.626 r_lrange_other 8.624 r_dihedral_angle_2_deg 7.721 r_scangle_it 7.145 r_scangle_other 7.143 r_dihedral_angle_1_deg 6.839 r_scbond_it 4.63 r_scbond_other 4.629 r_mcangle_it 3.465 r_mcangle_other 3.464 r_mcbond_it 2.342 r_mcbond_other 2.34 r_angle_refined_deg 1.935 r_angle_other_deg 0.651 r_nbd_refined 0.227 r_symmetry_nbd_other 0.202 r_nbd_other 0.188 r_nbtor_refined 0.182 r_symmetry_nbd_refined 0.144 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_refined 0.075 r_dihedral_angle_other_2_deg 0.024 r_bond_refined_d 0.011 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 56 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction