6SP7

Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in Complex with Taniborbactam (VNRX-5133)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KO3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M cacodilate (pH 6.5), 5 mM DTT , 0.2 M Na-acetate, 26% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.1342.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.91α = 90
b = 79.04β = 130.5
c = 67.49γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

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
11.855.60996.90.080.1140.0647.433688036880
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)
11.81.9960.3830.3830.5460.3081.93

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 REPLACEMENTTHROUGHOUT1KO31.828.9234979189496.70.19190.1890.2444RANDOM22.42
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.201
r_dihedral_angle_4_deg21.684
r_dihedral_angle_3_deg14.894
r_dihedral_angle_1_deg6.813
r_angle_refined_deg2.067
r_angle_other_deg1.116
r_chiral_restr0.175
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.201
r_dihedral_angle_4_deg21.684
r_dihedral_angle_3_deg14.894
r_dihedral_angle_1_deg6.813
r_angle_refined_deg2.067
r_angle_other_deg1.116
r_chiral_restr0.175
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3466
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction