9DWP | pdb_00009dwp

Crystal Structure of C4-Dicarboxylate-Binding Protein (PA0884) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with Mesaconic Acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5292Protein: 8.5 mg/ml, 0.15M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM Mesaconic Acid; Screen: PEGs II (D11), 0.2M Magnesium chloride, 0.1M Tris (pH 8.5), 30% (w/v) PEG 4000; Cryo: Reservoir
Crystal Properties
Matthews coefficientSolvent content
1.9336.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.52α = 90
b = 67.2β = 106.47
c = 60.469γ = 90
Symmetry
Space GroupP 1 21 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)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
11.323098.60.0890.0890.1030.0510.99714.53.761217-39.1
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)
11.321.3499.90.7710.7710.8950.4450.5752.13.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.3229.758148301298.420.158530.157570.16280.177270.1817RANDOM9.894
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]
-0.03-0.040.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg9.116
r_long_range_B_refined4.95
r_long_range_B_other4.695
r_dihedral_angle_1_deg4.26
r_scangle_other2.731
r_dihedral_angle_2_deg2.518
r_scbond_other1.69
r_scbond_it1.689
r_angle_refined_deg1.411
r_mcangle_other1.344
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg9.116
r_long_range_B_refined4.95
r_long_range_B_other4.695
r_dihedral_angle_1_deg4.26
r_scangle_other2.731
r_dihedral_angle_2_deg2.518
r_scbond_other1.69
r_scbond_it1.689
r_angle_refined_deg1.411
r_mcangle_other1.344
r_mcangle_it1.342
r_mcbond_it0.849
r_mcbond_other0.824
r_angle_other_deg0.485
r_chiral_restr0.076
r_gen_planes_refined0.017
r_gen_planes_other0.015
r_bond_refined_d0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2451
Nucleic Acid Atoms
Solvent Atoms451
Heterogen Atoms12

Software

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