2J44

Alpha-glucan binding by a streptococcal virulence factor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J43PDB ENTRY 2J43

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.3346.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.555α = 90
b = 89.124β = 90
c = 59.997γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU IMAGE PLATEMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
12.119.5196.90.0710.34.4158732
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)
12.12.1799.10.373.14.31

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 2J432.1201507080296.90.2250.2210.304RANDOM49.09
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]
-0.990.410.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.558
r_scangle_it3.816
r_scbond_it2.437
r_mcangle_it1.89
r_angle_refined_deg1.554
r_mcbond_it1.058
r_symmetry_vdw_refined0.329
r_nbd_refined0.234
r_xyhbond_nbd_refined0.209
r_symmetry_hbond_refined0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.558
r_scangle_it3.816
r_scbond_it2.437
r_mcangle_it1.89
r_angle_refined_deg1.554
r_mcbond_it1.058
r_symmetry_vdw_refined0.329
r_nbd_refined0.234
r_xyhbond_nbd_refined0.209
r_symmetry_hbond_refined0.17
r_chiral_restr0.118
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms1796
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
SPYDphasing