8BTW

Structure of D179N 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 DROP6.22930.1 M sodium phosphate buffer (pH 6.2); 0.2 M sodium formate; 20% v/v PEGSM
Crystal Properties
Matthews coefficientSolvent content
2.0138.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.819α = 90
b = 54.452β = 90
c = 79.517γ = 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 I04-10.979DiamondI04-1

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
11.944.9799.90.0970.98841.919008
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)
11.91.940.450.6031

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 REPLACEMENTTHROUGHOUT2GDN1.944.971816584299.870.162850.161020.20224RANDOM18.214
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]
-1.01-0.51.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.367
r_dihedral_angle_1_deg6.909
r_dihedral_angle_2_deg6.711
r_long_range_B_refined4.93
r_long_range_B_other4.753
r_scangle_other2.912
r_scbond_it2.126
r_scbond_other1.948
r_mcangle_it1.898
r_mcangle_other1.898
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.367
r_dihedral_angle_1_deg6.909
r_dihedral_angle_2_deg6.711
r_long_range_B_refined4.93
r_long_range_B_other4.753
r_scangle_other2.912
r_scbond_it2.126
r_scbond_other1.948
r_mcangle_it1.898
r_mcangle_other1.898
r_angle_refined_deg1.445
r_mcbond_it1.263
r_mcbond_other1.263
r_angle_other_deg0.478
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.005
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 Atoms185
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing