9HT4

Crystal structure of PA0884, the SBP component of a Pseudomonas aeruginosa PAO1 Tripartite ATP-independent Periplasmic (TRAP) transporter, complexed with succinate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAF-Q9I561-F1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293JCSG-plus HT-96 D12: 0.04 M Potassium phosphate monobasic, 16 % w/v PEG 8000, 20 % v/v Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.4148.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.957α = 90
b = 118.525β = 90
c = 167.21γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2023-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7550.441000.4020.4340.1650.9925.31369593
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)RedundancyNumber Unique Reflections (All)
11.751.785.215.6622.2050.19912.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.7550.4465952353099.960.203070.200970.24125RANDOM24.944
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]
-1.991.40.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.098
r_dihedral_angle_2_deg11.624
r_long_range_B_refined7.97
r_dihedral_angle_1_deg6.646
r_scbond_it5.417
r_mcangle_it3.862
r_mcbond_it2.985
r_angle_refined_deg2.553
r_chiral_restr0.159
r_bond_refined_d0.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.098
r_dihedral_angle_2_deg11.624
r_long_range_B_refined7.97
r_dihedral_angle_1_deg6.646
r_scbond_it5.417
r_mcangle_it3.862
r_mcbond_it2.985
r_angle_refined_deg2.553
r_chiral_restr0.159
r_bond_refined_d0.015
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4874
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing