4D70

Structural, biophysical and biochemical analyses of a Clostridium perfringens Sortase D5 transpeptidase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.5281THE PROTEIN CONCENTRATION WAS 20 MG/ML AND THE RESERVOIR CONDITIONS WERE 0.2M AMMONIUM ACETATE, 25% PEG 3350, 0.1M BIS-TRIS CHLORIDE AT PH 5.5 AND INCUBATED AT 8C.
Crystal Properties
Matthews coefficientSolvent content
2.4148.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.776α = 90
b = 65.582β = 93.86
c = 68.057γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2013-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX2Australian SynchrotronMX2

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
11.9947.299.50.07187.523533
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)
11.992.0997.10.633.27

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 3G661.9967.922304121499.50.177690.175690.21335RANDOM38.509
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]
1.080.4-0.85-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.917
r_dihedral_angle_3_deg14.053
r_dihedral_angle_4_deg8.386
r_long_range_B_refined8.33
r_long_range_B_other8.322
r_scangle_other7.437
r_dihedral_angle_1_deg5.745
r_scbond_it5.16
r_scbond_other5.158
r_mcangle_it4.474
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.917
r_dihedral_angle_3_deg14.053
r_dihedral_angle_4_deg8.386
r_long_range_B_refined8.33
r_long_range_B_other8.322
r_scangle_other7.437
r_dihedral_angle_1_deg5.745
r_scbond_it5.16
r_scbond_other5.158
r_mcangle_it4.474
r_mcangle_other4.474
r_mcbond_other3.527
r_mcbond_it3.526
r_angle_refined_deg1.687
r_angle_other_deg1.227
r_chiral_restr0.11
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.005
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 Atoms2526
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing