2Y7I

Structural basis for high arginine specificity in Salmonella typhimurium periplasmic binding protein STM4351.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LAHPDB ENTRY 1LAH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.418% PEG 8000, 100MM SODIUM CACODYLATE, 200MM ZINC ACETATE., pH 7.4
Crystal Properties
Matthews coefficientSolvent content
2.347.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.317α = 90
b = 56.331β = 100.17
c = 88.37γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray273IMAGE PLATEMAR scanner 345 mm plateMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.947.2899.80.117.96351562.421.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.9599.10.862.45.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 1LAH1.947.2835156185699.870.199490.198050.22602RANDOM27.965
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]
1.17-0.04-0.12-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.454
r_dihedral_angle_4_deg18.907
r_dihedral_angle_3_deg14.157
r_dihedral_angle_1_deg5.645
r_scangle_it2.194
r_scbond_it1.338
r_angle_refined_deg1.084
r_mcangle_it0.795
r_mcbond_it0.414
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.454
r_dihedral_angle_4_deg18.907
r_dihedral_angle_3_deg14.157
r_dihedral_angle_1_deg5.645
r_scangle_it2.194
r_scbond_it1.338
r_angle_refined_deg1.084
r_mcangle_it0.795
r_mcbond_it0.414
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_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_other
r_long_range_B_refined
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 Atoms3558
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing