5EW0

Crystal structure of the metallo-beta-lactamase Sfh-I in complex with the bisthiazolidine inhibitor L-CS319


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SD9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2M sodium acetate, 27% w/v PEG 3350, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
1.9536.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.77α = 90
b = 86.7β = 90.09
c = 72.23γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-01-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.319.4297.60.1187.65.891618
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3295.50.5214.29.9

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 REPLACEMENTTHROUGHOUT3SD91.319.4291618474296.980.161590.160180.18863RANDOM11.754
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]
-0.7-0.45-1.952.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.673
r_dihedral_angle_4_deg19.929
r_dihedral_angle_3_deg12.481
r_dihedral_angle_1_deg6.236
r_long_range_B_refined5.624
r_long_range_B_other5.322
r_scangle_other2.883
r_scbond_it1.97
r_scbond_other1.966
r_mcangle_it1.713
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.673
r_dihedral_angle_4_deg19.929
r_dihedral_angle_3_deg12.481
r_dihedral_angle_1_deg6.236
r_long_range_B_refined5.624
r_long_range_B_other5.322
r_scangle_other2.883
r_scbond_it1.97
r_scbond_other1.966
r_mcangle_it1.713
r_mcangle_other1.712
r_angle_refined_deg1.569
r_angle_other_deg1.441
r_mcbond_it1.14
r_mcbond_other1.14
r_chiral_restr0.096
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms3622
Nucleic Acid Atoms
Solvent Atoms603
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing