7PCI

BurG (holo) in complex with hydroxypyruvate-enol (8): 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 Imidazole; 20% PEG 6K, 2 mM NAD+, 5 mM MgCl2, 2 mM (8)
Crystal Properties
Matthews coefficientSolvent content
1.935.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.67α = 90
b = 84.47β = 90
c = 46.2γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-03-20MSINGLE 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
11.93098.40.07411.94.423699
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)
11.920.5692.7

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 REPLACEMENTTHROUGHOUT7PCC1.93022473118198.410.20010.19880.2251RANDOM28.13
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]
-4.12-2.036.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.564
r_dihedral_angle_4_deg13.973
r_dihedral_angle_3_deg13.001
r_dihedral_angle_1_deg6.126
r_angle_refined_deg1.215
r_angle_other_deg1.146
r_rigid_bond_restr0.754
r_chiral_restr0.043
r_gen_planes_refined0.003
r_bond_refined_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.564
r_dihedral_angle_4_deg13.973
r_dihedral_angle_3_deg13.001
r_dihedral_angle_1_deg6.126
r_angle_refined_deg1.215
r_angle_other_deg1.146
r_rigid_bond_restr0.754
r_chiral_restr0.043
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2633
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing