7PCC

BurG in complex with Mg2+ and NAD+ (holo): Biosynthesis of cyclopropanol rings in bacterial toxins


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4TSK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92930.1 M Bicine; 20% PEG 8K, 1 mM NAD+, 5 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.0640.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.49α = 90
b = 82.74β = 90
c = 100.87γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-08-29MSINGLE 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
11.853099.40.0968.84.454278
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)
11.851.950.572.5

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 REPLACEMENTTHROUGHOUT4TSK1.853051548271399.350.18690.18530.2165RANDOM22.772
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]
-1.4-3.314.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.442
r_dihedral_angle_4_deg17.414
r_dihedral_angle_3_deg13.408
r_dihedral_angle_1_deg6.18
r_angle_refined_deg1.204
r_angle_other_deg1.198
r_rigid_bond_restr0.622
r_chiral_restr0.05
r_bond_refined_d0.003
r_gen_planes_refined0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.442
r_dihedral_angle_4_deg17.414
r_dihedral_angle_3_deg13.408
r_dihedral_angle_1_deg6.18
r_angle_refined_deg1.204
r_angle_other_deg1.198
r_rigid_bond_restr0.622
r_chiral_restr0.05
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5221
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing