4GNR

1.0 Angstrom resolution crystal structure of the branched-chain amino acid transporter substrate binding protein LivJ from Streptococcus pneumoniae str. Canada MDR_19A in complex with Isoleucine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z18 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298Protein at 66 mg/mL, Crystallization condition: PEG 4K 30% w/v Mg Chloride 0.2M Tris0.1M, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0339.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.274α = 90
b = 72.819β = 105.1
c = 57.542γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBe-Lenses2012-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
113099.70.04822.854.5159549159549-37
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)
111.02980.4872.237818

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1z18127.78151086151086797699.690.127220.126220.14656RANDOM9.151
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]
0.07-0.10.09-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.509
r_dihedral_angle_3_deg8.186
r_dihedral_angle_4_deg6.454
r_scangle_it4.383
r_dihedral_angle_1_deg3.47
r_scbond_it2.917
r_mcbond_other2.572
r_mcangle_it2.105
r_angle_refined_deg1.747
r_mcbond_it1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.509
r_dihedral_angle_3_deg8.186
r_dihedral_angle_4_deg6.454
r_scangle_it4.383
r_dihedral_angle_1_deg3.47
r_scbond_it2.917
r_mcbond_other2.572
r_mcangle_it2.105
r_angle_refined_deg1.747
r_mcbond_it1.41
r_rigid_bond_restr1.317
r_angle_other_deg1.084
r_chiral_restr0.108
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2582
Nucleic Acid Atoms
Solvent Atoms613
Heterogen Atoms14

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling