7PCT

BurG E232Q mutant (holo) in complex with enol-oxalacetate (15): Biosynthesis of cyclopropanol rings in bacterial toxins


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 M Tris; o.2 M NaAc, 16% PEG 4K, 2 mM NAD+, 5 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.1542.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.29α = 90
b = 76.03β = 106.14
c = 78.23γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
11.353097.30.0688.13139870
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)
11.351.450.536

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 REPLACEMENTTHROUGHOUT7PCC1.3530132865699397.390.15730.15610.1795RANDOM13.772
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]
1.08-0.88-0.920.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.029
r_dihedral_angle_4_deg17.31
r_dihedral_angle_3_deg11.252
r_dihedral_angle_1_deg5.962
r_angle_other_deg1.477
r_angle_refined_deg1.437
r_rigid_bond_restr0.996
r_chiral_restr0.071
r_gen_planes_refined0.007
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.029
r_dihedral_angle_4_deg17.31
r_dihedral_angle_3_deg11.252
r_dihedral_angle_1_deg5.962
r_angle_other_deg1.477
r_angle_refined_deg1.437
r_rigid_bond_restr0.996
r_chiral_restr0.071
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5209
Nucleic Acid Atoms
Solvent Atoms749
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing