9DY3 | pdb_00009dy3

Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with L-Malate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9DSY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6292Protein: 7.0 mg/ml, 0.5M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM L-Malate; Screen: PACT (B8), 0.2 M Ammonium chloride, 0.1 M MES (pH 6.0), 20% (w/v) PEG 6000; Cryo: Reservoir
Crystal Properties
Matthews coefficientSolvent content
1.9637.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.505α = 78.95
b = 44.532β = 84.44
c = 46.886γ = 75.84
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2022-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.12723APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.33087.30.0470.0470.0280.99725.23.756875-311.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3271.60.3710.3710.4320.2210.8984.93.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.329.8453993288087.150.141670.140260.15010.167390.1759RANDOM18.43
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]
-0.39-0.15-0.03-0.960.311.4
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined12.965
r_long_range_B_other11.942
r_dihedral_angle_3_deg8.276
r_scangle_other7.455
r_mcangle_other5.907
r_mcangle_it5.905
r_scbond_other4.939
r_scbond_it4.938
r_dihedral_angle_1_deg4.524
r_mcbond_it4.057
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined12.965
r_long_range_B_other11.942
r_dihedral_angle_3_deg8.276
r_scangle_other7.455
r_mcangle_other5.907
r_mcangle_it5.905
r_scbond_other4.939
r_scbond_it4.938
r_dihedral_angle_1_deg4.524
r_mcbond_it4.057
r_mcbond_other4.048
r_dihedral_angle_2_deg2.573
r_rigid_bond_restr2.007
r_angle_refined_deg1.349
r_angle_other_deg0.474
r_chiral_restr0.074
r_gen_planes_refined0.01
r_gen_planes_other0.008
r_bond_refined_d0.005
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms2420
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing