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Crystal structure of SAR11_0655 bound to a co-purified ligand, L-pyroglutamate
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, HANGING DROP 3.5 293 1.5 uL 0.1 M sodium citrate pH 3.5, 0.15 M lithium sulfate, 16% (w/v) PEG 6000 + 1.5 uL 12 mg/mL protein. Cryoprotected in 0.1 M sodium citrate pH 3.5, 0.15 M lithium sulfate, 16% (w/v) PEG 6000, 30% (v/v) ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.74 55.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.204 α = 90 b = 122.204 β = 90 c = 125.908 γ = 90
Symmetry Space Group P 41 21 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 PIXEL DECTRIS EIGER X 9M 2023-06-28 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 1.519 43.846 99.9 0.133 0.136 0.999 14.89 20.9 146122
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 1.52 1.61 99.6 3.18 3.26 0.506 0.95
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold 1.519 41.304 146120 7328 99.917 0.152 0.1502 0.1867 0.1906 22.753
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] -0.04 -0.04 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.284 r_dihedral_angle_2_deg 14.518 r_dihedral_angle_3_deg 12.877 r_dihedral_angle_1_deg 6.098 r_rigid_bond_restr 3.788 r_lrange_it 3.035 r_lrange_other 2.736 r_scangle_it 2.382 r_scangle_other 2.382 r_mcangle_it 1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.284 r_dihedral_angle_2_deg 14.518 r_dihedral_angle_3_deg 12.877 r_dihedral_angle_1_deg 6.098 r_rigid_bond_restr 3.788 r_lrange_it 3.035 r_lrange_other 2.736 r_scangle_it 2.382 r_scangle_other 2.382 r_mcangle_it 1.96 r_mcangle_other 1.96 r_scbond_it 1.807 r_scbond_other 1.807 r_angle_refined_deg 1.569 r_mcbond_it 1.464 r_mcbond_other 1.464 r_angle_other_deg 0.565 r_symmetry_nbd_refined 0.317 r_symmetry_xyhbond_nbd_refined 0.253 r_nbd_refined 0.226 r_nbd_other 0.207 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.028 r_bond_refined_d 0.009 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 5952 Nucleic Acid Atoms Solvent Atoms 602 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing