2YL8

Inhibition of the pneumococcal virulence factor StrH and molecular insights into N-glycan recognition and hydrolysis


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.5151.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.57α = 90
b = 109.29β = 90
c = 112.93γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
11.7535.61000.0920.48492802
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)
11.751.841000.44.48

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.7535.646762249199.950.166470.164440.20522RANDOM14.374
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]
0.13-0.160.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.988
r_dihedral_angle_4_deg16.347
r_dihedral_angle_3_deg12.641
r_dihedral_angle_1_deg5.82
r_scangle_it3.903
r_scbond_it2.361
r_angle_refined_deg1.425
r_mcangle_it1.29
r_mcbond_it0.733
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.988
r_dihedral_angle_4_deg16.347
r_dihedral_angle_3_deg12.641
r_dihedral_angle_1_deg5.82
r_scangle_it3.903
r_scbond_it2.361
r_angle_refined_deg1.425
r_mcangle_it1.29
r_mcbond_it0.733
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_refined0.007
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 Atoms3397
Nucleic Acid Atoms
Solvent Atoms623
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing