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Crystal structure of Adenylosuccinate lyase from Thermus thermophilus HB8, TtPurB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 293 0.1M Sodium acetate trihydrate (pH 4.6),
1.0M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.69 54.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.657 α = 90 b = 158.657 β = 90 c = 151.634 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2007-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.37 50 100 0.077 30.8 11.2 86898
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.37 2.45 100 0.353 6.83 11.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.38 19.992 45475 2262 99.743 0.207 0.2047 0.2485 0.25 43.549
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] 0.001 0.001 0.001 -0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.648 r_dihedral_angle_4_deg 19.528 r_dihedral_angle_3_deg 18.217 r_lrange_other 10.621 r_lrange_it 10.609 r_scangle_it 8.306 r_scangle_other 8.302 r_dihedral_angle_1_deg 8.068 r_mcangle_it 5.928 r_mcangle_other 5.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.648 r_dihedral_angle_4_deg 19.528 r_dihedral_angle_3_deg 18.217 r_lrange_other 10.621 r_lrange_it 10.609 r_scangle_it 8.306 r_scangle_other 8.302 r_dihedral_angle_1_deg 8.068 r_mcangle_it 5.928 r_mcangle_other 5.927 r_scbond_it 5.579 r_scbond_other 5.574 r_mcbond_it 4.366 r_mcbond_other 4.366 r_angle_refined_deg 1.714 r_angle_other_deg 1.405 r_symmetry_nbd_refined 0.33 r_symmetry_xyhbond_nbd_refined 0.241 r_nbd_refined 0.233 r_nbd_other 0.216 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.023 r_bond_refined_d 0.011 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 4860 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing