8BTV

Structure of D179N BlaC from Mycobacterium tuberculosis bound to the trans-enamine adduct of sulbactam


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6H2K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.1 M sodium phosphate/citrate (pH 5.5); 20% v/v PEGSH
Crystal Properties
Matthews coefficientSolvent content
2.0239.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.945α = 90
b = 54.727β = 92.86
c = 53.879γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2020-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9795DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
11.9353.8799.80.0850.9894.31.917094
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.931.980.380.683

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 REPLACEMENTTHROUGHOUT6H2K1.9553.871584378699.940.172690.170990.20684RANDOM17.684
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]
0.430.3-0.27-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.609
r_dihedral_angle_2_deg8.715
r_dihedral_angle_1_deg6.856
r_long_range_B_refined4.416
r_long_range_B_other4.359
r_scangle_other2.575
r_scbond_it1.813
r_scbond_other1.793
r_mcangle_it1.756
r_mcangle_other1.755
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.609
r_dihedral_angle_2_deg8.715
r_dihedral_angle_1_deg6.856
r_long_range_B_refined4.416
r_long_range_B_other4.359
r_scangle_other2.575
r_scbond_it1.813
r_scbond_other1.793
r_mcangle_it1.756
r_mcangle_other1.755
r_angle_refined_deg1.397
r_mcbond_it1.158
r_mcbond_other1.158
r_angle_other_deg0.471
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1992
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing