8WCH

Crystal structure of SAR11_0655 bound to a co-purified ligand, L-pyroglutamate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.52931.5 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 coefficientSolvent content
2.7455.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.204α = 90
b = 122.204β = 90
c = 125.908γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2023-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1.000SPring-8BL32XU

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.51943.84699.90.1330.1360.99914.8920.9146122
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)RedundancyNumber Unique Reflections (All)
11.521.6199.63.183.260.5060.95

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEAlphaFold1.51941.304146120732899.9170.1520.15020.186722.753
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]
-0.04-0.040.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.284
r_dihedral_angle_2_deg14.518
r_dihedral_angle_3_deg12.877
r_dihedral_angle_1_deg6.098
r_rigid_bond_restr3.788
r_lrange_it3.035
r_lrange_other2.736
r_scangle_it2.382
r_scangle_other2.382
r_mcangle_it1.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.284
r_dihedral_angle_2_deg14.518
r_dihedral_angle_3_deg12.877
r_dihedral_angle_1_deg6.098
r_rigid_bond_restr3.788
r_lrange_it3.035
r_lrange_other2.736
r_scangle_it2.382
r_scangle_other2.382
r_mcangle_it1.96
r_mcangle_other1.96
r_scbond_it1.807
r_scbond_other1.807
r_angle_refined_deg1.569
r_mcbond_it1.464
r_mcbond_other1.464
r_angle_other_deg0.565
r_symmetry_nbd_refined0.317
r_symmetry_xyhbond_nbd_refined0.253
r_nbd_refined0.226
r_nbd_other0.207
r_symmetry_nbd_other0.19
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.145
r_chiral_restr0.085
r_symmetry_nbtor_other0.082
r_symmetry_xyhbond_nbd_other0.028
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5952
Nucleic Acid Atoms
Solvent Atoms602
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing