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Crystal structure of SAR11_0769 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to a co-purified ligand, beta-galactopyranose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HQQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 20% (v/v) 2-propanol, 0.1 M MES pH 6.5, 23% (w/v) PEG 1500. 1.2 uL protein + 1.2 uL precipitant.
Crystal Properties Matthews coefficient Solvent content 2.14 42.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.879 α = 90 b = 43.879 β = 90 c = 328.555 γ = 120
Symmetry Space Group P 32 2 1
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 9M 2023-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.67 46.936 99.6 0.135 0.141 0.997 11.08 12.2 43960
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.78 97.3 1.608 1.683 0.864 1.05 11.37
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 8HQQ 1.675 38.029 43950 2217 99.547 0.195 0.1937 0.2039 0.2288 0.2396 40.44
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] 1.066 0.533 1.066 -3.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.733 r_dihedral_angle_3_deg 15.653 r_dihedral_angle_2_deg 15.328 r_dihedral_angle_1_deg 6.252 r_lrange_it 4.404 r_lrange_other 4.401 r_scangle_it 3.909 r_scangle_other 3.908 r_scbond_it 2.664 r_scbond_other 2.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.733 r_dihedral_angle_3_deg 15.653 r_dihedral_angle_2_deg 15.328 r_dihedral_angle_1_deg 6.252 r_lrange_it 4.404 r_lrange_other 4.401 r_scangle_it 3.909 r_scangle_other 3.908 r_scbond_it 2.664 r_scbond_other 2.663 r_mcangle_it 2.368 r_mcangle_other 2.368 r_mcbond_it 1.864 r_mcbond_other 1.857 r_angle_refined_deg 1.368 r_angle_other_deg 0.484 r_nbd_refined 0.215 r_symmetry_nbd_refined 0.208 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.159 r_nbd_other 0.139 r_xyhbond_nbd_refined 0.118 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.067 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2933 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing