5TRO

1.8 Angstrom Resolution Crystal Structure of Dimerization and Transpeptidase domains (residues 39-608) of Penicillin-Binding Protein 1 from Staphylococcus aureus.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.3295Protein: 10.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), Screen: JCSG+ (A5), 0.2M Magnesium formate, 20% (w/v) PEG 3350.
Crystal Properties
Matthews coefficientSolvent content
2.1141.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.843α = 90
b = 72.202β = 103.18
c = 86.362γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2016-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.83099.70.0880.08826.85.498204-330.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8399.30.7490.7932.34.9

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 DIFFRACTIONSADTHROUGHOUT1.829.5993238495099.220.180880.179350.20946RANDOM43.7
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]
0.34-1.07-1.381.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.828
r_dihedral_angle_4_deg10.696
r_dihedral_angle_3_deg10.411
r_long_range_B_refined5.186
r_long_range_B_other5.028
r_dihedral_angle_1_deg3.139
r_scangle_other1.941
r_mcangle_it1.739
r_mcangle_other1.739
r_angle_refined_deg1.365
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.828
r_dihedral_angle_4_deg10.696
r_dihedral_angle_3_deg10.411
r_long_range_B_refined5.186
r_long_range_B_other5.028
r_dihedral_angle_1_deg3.139
r_scangle_other1.941
r_mcangle_it1.739
r_mcangle_other1.739
r_angle_refined_deg1.365
r_scbond_it1.183
r_scbond_other1.183
r_mcbond_it1.066
r_mcbond_other1.065
r_angle_other_deg0.819
r_chiral_restr0.085
r_gen_planes_refined0.021
r_gen_planes_other0.017
r_bond_refined_d0.009
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7959
Nucleic Acid Atoms
Solvent Atoms615
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing