7PJ5

Crystal structure of catalytic domain of LytB from Streptococcus pneumoniae in complex with NAG-NAG-NAG-NAG tetrasaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7PJ3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291.15PEG 300 Bis-Tris Calcium acetate
Crystal Properties
Matthews coefficientSolvent content
2.2144.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.679α = 90
b = 92.358β = 90
c = 124.3γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979260ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.5546.181000.0580.01724.512.840276
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.580.7010.199

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7PJ31.5546.17440235199199.9750.1460.14360.191723.592
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]
1.171-1.6720.501
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.094
r_dihedral_angle_4_deg23.472
r_dihedral_angle_3_deg12.753
r_dihedral_angle_1_deg6.598
r_rigid_bond_restr5.724
r_scangle_it4.184
r_scangle_other4.183
r_lrange_it4.17
r_lrange_other4.102
r_scbond_it3.661
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.094
r_dihedral_angle_4_deg23.472
r_dihedral_angle_3_deg12.753
r_dihedral_angle_1_deg6.598
r_rigid_bond_restr5.724
r_scangle_it4.184
r_scangle_other4.183
r_lrange_it4.17
r_lrange_other4.102
r_scbond_it3.661
r_scbond_other3.66
r_mcangle_other3.103
r_mcangle_it3.1
r_mcbond_it2.769
r_mcbond_other2.741
r_angle_other_deg1.931
r_angle_refined_deg1.668
r_nbd_other0.323
r_symmetry_nbd_refined0.258
r_symmetry_metal_ion_refined0.229
r_symmetry_xyhbond_nbd_refined0.212
r_nbd_refined0.208
r_symmetry_nbd_other0.206
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.152
r_metal_ion_refined0.119
r_symmetry_xyhbond_nbd_other0.111
r_chiral_restr0.091
r_symmetry_nbtor_other0.082
r_bond_other_d0.018
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2174
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing