7PCL

BurG (holo) in complex with 2-hydroxy-2-(hydroxy(isopropyl)amino)acetate (11): Biosynthesis of cyclopropanolrings 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 DROP2930.1 M Tris; 0.8 M LiCl, 8% PEG 4K, 2 mM NADH, 5 mM MgCl2, 2 mM 11
Crystal Properties
Matthews coefficientSolvent content
2.0941.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.71α = 90
b = 84.04β = 90
c = 101.83γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-11-08MSINGLE 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
12.053097.80.0978.53.840538
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)
12.052.150.5583.1

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 REPLACEMENTTHROUGHOUT7PCC2.053038498202697.780.18950.1880.2181RANDOM23.579
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]
-3.23-0.73.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.12
r_dihedral_angle_4_deg18.093
r_dihedral_angle_3_deg13.523
r_dihedral_angle_1_deg6.076
r_angle_refined_deg1.255
r_angle_other_deg1.151
r_rigid_bond_restr0.367
r_chiral_restr0.046
r_gen_planes_refined0.003
r_bond_refined_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.12
r_dihedral_angle_4_deg18.093
r_dihedral_angle_3_deg13.523
r_dihedral_angle_1_deg6.076
r_angle_refined_deg1.255
r_angle_other_deg1.151
r_rigid_bond_restr0.367
r_chiral_restr0.046
r_gen_planes_refined0.003
r_bond_refined_d0.002
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 Atoms220
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing