7PCG

BurG (holo) in complex with cyclopropane-1,1-dicarboxylate (7): 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; 20% PEG 10K, 2 mM NAD+, 5 mM MgCl2. 2mM (7)
Crystal Properties
Matthews coefficientSolvent content
2.0640.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.63α = 90
b = 83.26β = 90
c = 101.21γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-09-12MSINGLE 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
11.93097.70.08510.24.249898
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)
11.9299.50.5712.1

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 REPLACEMENTTHROUGHOUT7PCC1.93047391249497.710.19740.19520.2282RANDOM27.451
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]
-0.03-0.660.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.426
r_dihedral_angle_4_deg16.613
r_dihedral_angle_3_deg13.415
r_dihedral_angle_1_deg5.879
r_angle_refined_deg1.198
r_angle_other_deg1.17
r_rigid_bond_restr0.399
r_chiral_restr0.049
r_bond_refined_d0.004
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.426
r_dihedral_angle_4_deg16.613
r_dihedral_angle_3_deg13.415
r_dihedral_angle_1_deg5.879
r_angle_refined_deg1.198
r_angle_other_deg1.17
r_rigid_bond_restr0.399
r_chiral_restr0.049
r_bond_refined_d0.004
r_bond_other_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5221
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing