8BV4

Structure of BlaC from Mycobacterium tuberculosis in complex with vaborbactam


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GDN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1M MES/Imidazole buffer pH 8.5, 30% w/v EDO-P8K, 0.09M NPS (sodium nitrate, disodium hydrogen phosphate, ammonium sulfate)
Crystal Properties
Matthews coefficientSolvent content
2.0138.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.49α = 90
b = 54.656β = 90
c = 78.109γ = 90
Symmetry
Space GroupP 21 21 21

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
11.9544.8299.90.1240.9856.51.917259
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)
11.9520.5660.7031.3

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 REPLACEMENTTHROUGHOUT2GDN1.9544.821640884799.930.190270.188220.22972RANDOM28.154
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]
-3.05-36.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.496
r_dihedral_angle_2_deg6.901
r_dihedral_angle_1_deg6.878
r_long_range_B_refined6.615
r_long_range_B_other6.316
r_scangle_other3.858
r_mcangle_it3.035
r_mcangle_other3.034
r_scbond_it3.011
r_scbond_other2.689
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.496
r_dihedral_angle_2_deg6.901
r_dihedral_angle_1_deg6.878
r_long_range_B_refined6.615
r_long_range_B_other6.316
r_scangle_other3.858
r_mcangle_it3.035
r_mcangle_other3.034
r_scbond_it3.011
r_scbond_other2.689
r_mcbond_it2.168
r_mcbond_other2.161
r_angle_refined_deg1.523
r_angle_other_deg0.495
r_chiral_restr0.066
r_bond_refined_d0.008
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 Atoms1988
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing