7QXC

Recognition of Staphylococcus aureus wall teichoic acid analogue SA533 (compound 1) by Fab4461


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5I1Dseparate constant and variable domains of PDB entry 5I1D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.529410 mM Tris-HCl; 250 mM sodium chloride; 12.9 % w/v polyethylene glycol 20,000; 150 mM CAPSO pH 9.5; 6 % v/v polyethylene glycol 300
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.191α = 90
b = 65.448β = 112.899
c = 74.338γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97926ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.4553.5196.60.0280.0390.0270.99716.43.18765621.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.5380.60.430.5930.4060.6081.52.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEseparate constant and variable domains of PDB entry 5I1D1.45253.5187588436896.540.1760.17430.199923.016
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]
-0.415-0.0610.1010.269
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.742
r_dihedral_angle_4_deg21.132
r_dihedral_angle_3_deg11.908
r_dihedral_angle_1_deg7.152
r_lrange_it6.356
r_lrange_other6.302
r_scangle_it4.08
r_scangle_other4.079
r_mcangle_it3.201
r_mcangle_other3.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.742
r_dihedral_angle_4_deg21.132
r_dihedral_angle_3_deg11.908
r_dihedral_angle_1_deg7.152
r_lrange_it6.356
r_lrange_other6.302
r_scangle_it4.08
r_scangle_other4.079
r_mcangle_it3.201
r_mcangle_other3.2
r_scbond_it2.613
r_scbond_other2.613
r_mcbond_it1.943
r_mcbond_other1.94
r_angle_refined_deg1.498
r_angle_other_deg1.352
r_symmetry_nbd_refined0.237
r_symmetry_xyhbond_nbd_refined0.231
r_xyhbond_nbd_refined0.221
r_nbd_refined0.197
r_symmetry_nbd_other0.178
r_nbtor_refined0.163
r_nbd_other0.121
r_xyhbond_nbd_other0.084
r_symmetry_nbtor_other0.077
r_chiral_restr0.069
r_symmetry_xyhbond_nbd_other0.048
r_chiral_restr_other0.029
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3317
Nucleic Acid Atoms
Solvent Atoms424
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing