5LJL

Streptococcus pneumonia TIGR4 flavodoxin: structural and biophysical characterization of a novel drug target


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LJI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5292100mM Bis-Tris pH 5.5 and 200 mM calcium chloride, and 10% glycerol
Crystal Properties
Matthews coefficientSolvent content
1.7329.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 29.871α = 90
b = 60.707β = 90
c = 61.803γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2013-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.62099.20.1020.99813.99.915310

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 REPLACEMENTTHROUGHOUT5Lji1.661.81483743398.920.173750.172570.21532RANDOM16.596
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]
2-0.49-1.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.018
r_dihedral_angle_4_deg31.757
r_dihedral_angle_3_deg13.607
r_dihedral_angle_1_deg5.925
r_long_range_B_refined5.662
r_long_range_B_other5.624
r_scangle_other5.047
r_scbond_other3.329
r_scbond_it3.321
r_mcangle_other2.279
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.018
r_dihedral_angle_4_deg31.757
r_dihedral_angle_3_deg13.607
r_dihedral_angle_1_deg5.925
r_long_range_B_refined5.662
r_long_range_B_other5.624
r_scangle_other5.047
r_scbond_other3.329
r_scbond_it3.321
r_mcangle_other2.279
r_mcangle_it2.261
r_angle_refined_deg1.874
r_mcbond_it1.5
r_mcbond_other1.462
r_angle_other_deg1.16
r_chiral_restr0.168
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms1121
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing