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Crystal structure of the arginine-/lysine-binding protein SAR11_1210 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OT8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 1 uL 12 mg/mL protein + 1 uL 21% (w/v) PEG 1500, 0.1 M MES pH 6.0. Final crystal obtained by serial microseeding from this condition. Crystal cryoprotected in 30% (w/v) PEG 1500, 0.1 M MES pH 6.0.
Crystal Properties Matthews coefficient Solvent content 2.15 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.128 α = 90 b = 84.689 β = 90 c = 106.097 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 100 PIXEL DECTRIS EIGER X 9M 2022-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.000 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 1.32 47.4 99.4 0.123 0.129 0.996 10.44 12.2 121098
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 1.32 1.4 99.1 1.411 1.476 0.709 1.16 11.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5OT8 1.32 47.4 114968 6128 99.42 0.15094 0.1489 0.1471 0.19047 0.1875 RANDOM 20.203
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] -1.4 3.6 -2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.902 r_rigid_bond_restr 12.751 r_dihedral_angle_2_deg 10.865 r_long_range_B_refined 8.412 r_long_range_B_other 8.376 r_scangle_other 8.159 r_mcbond_it 7.82 r_mcbond_other 7.82 r_mcangle_it 7.633 r_mcangle_other 7.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.902 r_rigid_bond_restr 12.751 r_dihedral_angle_2_deg 10.865 r_long_range_B_refined 8.412 r_long_range_B_other 8.376 r_scangle_other 8.159 r_mcbond_it 7.82 r_mcbond_other 7.82 r_mcangle_it 7.633 r_mcangle_other 7.631 r_scbond_it 7.614 r_scbond_other 7.612 r_dihedral_angle_1_deg 5.762 r_angle_refined_deg 1.525 r_angle_other_deg 0.563 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3865 Nucleic Acid Atoms Solvent Atoms 578 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing