7PCO

BurG E232Q mutant (holo) in complex with 2R,3R-2,3-dihydroxy-6-methyl-heptanoate (12): 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 DROP7.52930.1 M NaAc; 0.05 M M MgAc2, 10% PEG 8K, 2 mM NAD+, 5 mM MgCl2, 2 mM (12)
Crystal Properties
Matthews coefficientSolvent content
2.1442.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.73α = 90
b = 83.4β = 90
c = 104.78γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 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
11.553096.40.0828.13.593303
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)
11.551.650.5492

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 REPLACEMENTTHROUGHOUT7PCC1.553088624466596.390.17750.17620.1993RANDOM17.668
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]
-0.59-0.631.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.677
r_dihedral_angle_4_deg17.177
r_dihedral_angle_3_deg12.689
r_dihedral_angle_1_deg6.149
r_angle_refined_deg1.429
r_angle_other_deg1.402
r_rigid_bond_restr1.027
r_chiral_restr0.073
r_bond_refined_d0.006
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.677
r_dihedral_angle_4_deg17.177
r_dihedral_angle_3_deg12.689
r_dihedral_angle_1_deg6.149
r_angle_refined_deg1.429
r_angle_other_deg1.402
r_rigid_bond_restr1.027
r_chiral_restr0.073
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5219
Nucleic Acid Atoms
Solvent Atoms423
Heterogen Atoms123

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing