7PCN

BurG (holo) in complex with gonyenediol (14), trigonic acid (6) and DMS: 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 DROP82930.1 M Inidazole; 10% PEG 8K, 2 mM NAD+, 5 mM MgCl2, 2 mM gonydiol (5)
Crystal Properties
Matthews coefficientSolvent content
2.141.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.88α = 90
b = 76.13β = 105.14
c = 79.11γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-01-31MSINGLE 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
11.63098.20.0917.33.182909
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)
11.61.70.5731.9

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 REPLACEMENTTHROUGHOUT7PCC1.63078752414598.270.1350.13370.1594RANDOM17.986
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]
0.68-0.55-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.011
r_dihedral_angle_4_deg19.017
r_dihedral_angle_3_deg12.128
r_dihedral_angle_1_deg6.04
r_rigid_bond_restr1.589
r_angle_refined_deg1.442
r_angle_other_deg1.417
r_chiral_restr0.075
r_bond_refined_d0.006
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.011
r_dihedral_angle_4_deg19.017
r_dihedral_angle_3_deg12.128
r_dihedral_angle_1_deg6.04
r_rigid_bond_restr1.589
r_angle_refined_deg1.442
r_angle_other_deg1.417
r_chiral_restr0.075
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5225
Nucleic Acid Atoms
Solvent Atoms473
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing