☰ Navigation Tabs
Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 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 15%(v/v)PEG#200, 0.1 M phosphate citrate pH 5.4
Crystal Properties Matthews coefficient Solvent content 2.19770145 44.0672035
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.953 α = 90 b = 77.953 β = 90 c = 231.05 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 43.89 100 0.109 0.122 0.053 0.998 12.8 10.1 57204
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 1.39 100 0.873 0.987 0.454 0.677 2.6 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 1.37 43.89 57203 2787 99.976 0.121 0.1192 0.1194 0.1461 0.1457 14.744
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] 0.046 0.023 0.046 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.763 r_dihedral_angle_2_deg 12.853 r_lrange_it 12.273 r_lrange_other 12.152 r_dihedral_angle_3_deg 11.469 r_scangle_it 10.112 r_scangle_other 10.109 r_scbond_it 7.556 r_scbond_other 7.555 r_dihedral_angle_1_deg 6.778
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.763 r_dihedral_angle_2_deg 12.853 r_lrange_it 12.273 r_lrange_other 12.152 r_dihedral_angle_3_deg 11.469 r_scangle_it 10.112 r_scangle_other 10.109 r_scbond_it 7.556 r_scbond_other 7.555 r_dihedral_angle_1_deg 6.778 r_mcangle_it 5.159 r_mcangle_other 5.158 r_rigid_bond_restr 4.382 r_mcbond_it 3.574 r_mcbond_other 3.567 r_angle_refined_deg 1.846 r_angle_other_deg 0.644 r_nbd_refined 0.221 r_symmetry_nbd_other 0.212 r_nbd_other 0.203 r_dihedral_angle_other_2_deg 0.188 r_symmetry_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.177 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.012 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 112 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction