6SP6

Ultra-high Resolution Crystal Structure of the CTX-M-15 Extended-Spectrum beta-Lactamase in Complex with Taniborbactam (VNRX-5133)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HBT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1M Tris-HCl, 2.2-2.4M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.1342.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.558α = 90
b = 45.719β = 90
c = 117.219γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2015-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.158.6198.90.0750.0830.03511.65.39683796837
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.1697.50.3040.3040.3370.1442.55.3

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 REPLACEMENTTHROUGHOUT4HBT1.158.6192020474698.760.10260.10160.1208RANDOM12.099
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free52.044
r_dihedral_angle_2_deg37.272
r_sphericity_bonded14.434
r_dihedral_angle_3_deg11.969
r_dihedral_angle_4_deg11.775
r_rigid_bond_restr6.73
r_dihedral_angle_1_deg5.9
r_angle_refined_deg2.16
r_angle_other_deg1.124
r_chiral_restr0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free52.044
r_dihedral_angle_2_deg37.272
r_sphericity_bonded14.434
r_dihedral_angle_3_deg11.969
r_dihedral_angle_4_deg11.775
r_rigid_bond_restr6.73
r_dihedral_angle_1_deg5.9
r_angle_refined_deg2.16
r_angle_other_deg1.124
r_chiral_restr0.15
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_bond_other_d0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1957
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction