7PCM

BurG (holo) in complex with (Z)-2,3-dihydroxy-6-methyl-hept-2-enoate (13): 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; 0.8 M LiCl, 8% PEG 4K, 2 mM NAD+, 5 mM MgCl2, 2 mM 13
Crystal Properties
Matthews coefficientSolvent content
2.0640.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.81α = 90
b = 83.61β = 90
c = 100.73γ = 90
Symmetry
Space GroupP 21 21 21

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
12.053098.50.1127.44.440243
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)
12.052.150.5962.4

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 REPLACEMENTTHROUGHOUT7PCC2.053038214201298.480.20530.20340.239RANDOM28.561
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]
-0.84-1.872.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.418
r_dihedral_angle_4_deg16.766
r_dihedral_angle_3_deg13.56
r_dihedral_angle_1_deg6.363
r_angle_refined_deg1.293
r_angle_other_deg1.173
r_rigid_bond_restr0.67
r_chiral_restr0.052
r_gen_planes_refined0.004
r_bond_refined_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.418
r_dihedral_angle_4_deg16.766
r_dihedral_angle_3_deg13.56
r_dihedral_angle_1_deg6.363
r_angle_refined_deg1.293
r_angle_other_deg1.173
r_rigid_bond_restr0.67
r_chiral_restr0.052
r_gen_planes_refined0.004
r_bond_refined_d0.003
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 Atoms111
Heterogen Atoms117

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing