5MLT

Structural characterization of a carbohydrate substrate binding protein from Streptococcus pneumoniae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.02 M Mes pH 6.5, 0.2 M NaCl, 2.5% glycerol and 0.5 mM TCEP
Crystal Properties
Matthews coefficientSolvent content
2.2745.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.24α = 90
b = 82.54β = 107.76
c = 60.35γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB mirrors2016-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.6149.6499.90.0230.0280.99916.46.66291320.01
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.611.6599.60.4430.57846.9

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.6149.6459803315899.940.194690.192920.22871RANDOM25.227
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.326
r_dihedral_angle_4_deg18.735
r_dihedral_angle_3_deg12.85
r_long_range_B_refined6.192
r_long_range_B_other6.013
r_dihedral_angle_1_deg5.87
r_scangle_other3.404
r_mcangle_it2.72
r_mcangle_other2.719
r_scbond_it2.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.326
r_dihedral_angle_4_deg18.735
r_dihedral_angle_3_deg12.85
r_long_range_B_refined6.192
r_long_range_B_other6.013
r_dihedral_angle_1_deg5.87
r_scangle_other3.404
r_mcangle_it2.72
r_mcangle_other2.719
r_scbond_it2.081
r_scbond_other2.081
r_mcbond_it1.661
r_mcbond_other1.659
r_angle_refined_deg1.389
r_angle_other_deg0.93
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms3583
Nucleic Acid Atoms
Solvent Atoms338
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
SHELXCDphasing