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Crystal structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 100K
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 VAPOR DIFFUSION, HANGING DROP 5.4 293.2 15%(v/v)PEG#200, 0.1 M phosphate citrate pH 5.4, 5 mM MTA
Crystal Properties Matthews coefficient Solvent content 2.18040133 43.6234131
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.766 α = 90 b = 77.766 β = 90 c = 230.335 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 100 PIXEL DECTRIS EIGER X 16M 2024-10-30 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 1.37 43.77 100 0.095 0.106 0.046 0.998 13.7 10 56744
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) 1.37 1.4 99.9 0.823 0.928 0.419 0.672 2.7 9.1
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 1.37 43.77 56742 2771 99.923 0.122 0.1208 0.1208 0.1472 0.1472 16.764
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] 0.162 0.081 0.162 -0.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.148 r_dihedral_angle_2_deg 13.505 r_lrange_it 13.442 r_lrange_other 13.407 r_dihedral_angle_3_deg 12.418 r_scangle_it 10.66 r_scangle_other 10.657 r_scbond_it 7.685 r_scbond_other 7.682 r_dihedral_angle_1_deg 7.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.148 r_dihedral_angle_2_deg 13.505 r_lrange_it 13.442 r_lrange_other 13.407 r_dihedral_angle_3_deg 12.418 r_scangle_it 10.66 r_scangle_other 10.657 r_scbond_it 7.685 r_scbond_other 7.682 r_dihedral_angle_1_deg 7.006 r_mcangle_it 6.592 r_mcangle_other 6.59 r_mcbond_it 4.551 r_mcbond_other 4.545 r_rigid_bond_restr 4.345 r_angle_refined_deg 2.007 r_angle_other_deg 0.67 r_nbd_other 0.26 r_symmetry_nbd_refined 0.223 r_nbd_refined 0.222 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.108 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.089 r_symmetry_xyhbond_nbd_refined 0.087 r_dihedral_angle_other_2_deg 0.047 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 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 96 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction