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Crystal structure of AziU3/U2 complexed with (5S,6S)-O7-sulfo DADH from Streptomyces sahachiroi
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 20% PEG 3350, 0.2M Magnesium formic acid
Crystal Properties Matthews coefficient Solvent content 2.22 44.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.872 α = 90 b = 131.756 β = 90 c = 157.702 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS3 6M 2021-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.8 48.873 99.6 0.05 0.06 0.032 0.999 20.4 6.3 106322
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 1.8 1.83 0.26 0.283 0.11 0.965 6.5
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 SAD FREE R-VALUE 1.8 48.873 106241 5387 99.486 0.165 0.1637 0.1934 0.1945 18.828
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] -0.603 -0.278 0.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.135 r_dihedral_angle_4_deg 14.785 r_dihedral_angle_3_deg 11.654 r_dihedral_angle_1_deg 6.563 r_lrange_it 3.317 r_lrange_other 3.315 r_scangle_it 1.258 r_scangle_other 1.258 r_angle_other_deg 1.214 r_angle_refined_deg 1.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.135 r_dihedral_angle_4_deg 14.785 r_dihedral_angle_3_deg 11.654 r_dihedral_angle_1_deg 6.563 r_lrange_it 3.317 r_lrange_other 3.315 r_scangle_it 1.258 r_scangle_other 1.258 r_angle_other_deg 1.214 r_angle_refined_deg 1.196 r_mcangle_it 1.026 r_mcangle_other 1.026 r_scbond_it 0.762 r_scbond_other 0.762 r_mcbond_it 0.616 r_mcbond_other 0.615 r_nbd_refined 0.19 r_nbd_other 0.169 r_symmetry_nbd_other 0.167 r_nbtor_refined 0.155 r_symmetry_nbd_refined 0.153 r_xyhbond_nbd_refined 0.115 r_symmetry_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.05 r_symmetry_xyhbond_nbd_other 0.021 r_metal_ion_refined 0.009 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8153 Nucleic Acid Atoms Solvent Atoms 1075 Heterogen Atoms 58
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement