4AZ6

Differential inhibition of the tandem GH20 catalytic modules in the pneumococcal exo-beta-D-N-acetylglucosaminidase, StrH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YL6PDB ENTRY 2YL6

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.550.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.3α = 90
b = 109.6β = 90
c = 112.6γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE 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
11.3628.8190.10.0719.19.8932672
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)
11.361.4357.70.3845.5

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 2YL61.3678.5688573469289.830.11640.115120.13999RANDOM13.024
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]
0.43-0.22-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.563
r_dihedral_angle_2_deg35.538
r_dihedral_angle_4_deg14.983
r_dihedral_angle_3_deg11.421
r_sphericity_bonded8.46
r_dihedral_angle_1_deg5.785
r_rigid_bond_restr3.096
r_angle_refined_deg1.36
r_angle_other_deg0.894
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.563
r_dihedral_angle_2_deg35.538
r_dihedral_angle_4_deg14.983
r_dihedral_angle_3_deg11.421
r_sphericity_bonded8.46
r_dihedral_angle_1_deg5.785
r_rigid_bond_restr3.096
r_angle_refined_deg1.36
r_angle_other_deg0.894
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3402
Nucleic Acid Atoms
Solvent Atoms652
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing