8A76

Metallo-beta-lactamase NDM-1 in complex with 1,2,4-Triazole-3-thione compound 26


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.3 M MgCl2 exahydrate; 0.3 M CaCl2 dihydrate; 25% w/v PEG 3350; 25% w/v MPD; 20% v/v PEG 1000; 0.1 M MES/IMIDAZOLE pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.0640.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.332α = 90
b = 73.904β = 90
c = 77.288γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2022-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.8856ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.542.571000.078121.518.365206
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.530.9

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 REPLACEMENTTHROUGHOUT6TGD1.542.5761894324199.940.16690.16580.1881RANDOM23.033
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]
1.18-1.440.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.416
r_dihedral_angle_4_deg19.943
r_dihedral_angle_3_deg13.639
r_dihedral_angle_1_deg6.745
r_angle_refined_deg1.95
r_chiral_restr0.116
r_bond_refined_d0.012
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3434
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing