5B15

Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Doripenem


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG4000, Ammonium sulfate, Tris-Hydrochloride
Crystal Properties
Matthews coefficientSolvent content
2.3242.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.01α = 107.57
b = 40.92β = 102.56
c = 45.32γ = 107.01
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAichiSR BEAMLINE BL2S11.12AichiSRBL2S1

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
11.3940.786.60.0412.81.939572
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)
11.391.4784.70.0721.91.9

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 REPLACEMENTTHROUGHOUT3VPE1.3940.737585198686.630.137610.136460.15829RANDOM10.434
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]
-0.070.39-0.280.92-0.39-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.129
r_dihedral_angle_4_deg19.258
r_dihedral_angle_3_deg12.875
r_dihedral_angle_1_deg7.137
r_long_range_B_refined5.024
r_long_range_B_other5.023
r_scangle_other3.278
r_scbond_it2.239
r_scbond_other2.238
r_angle_refined_deg1.589
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.129
r_dihedral_angle_4_deg19.258
r_dihedral_angle_3_deg12.875
r_dihedral_angle_1_deg7.137
r_long_range_B_refined5.024
r_long_range_B_other5.023
r_scangle_other3.278
r_scbond_it2.239
r_scbond_other2.238
r_angle_refined_deg1.589
r_mcangle_other1.507
r_mcangle_it1.506
r_mcbond_it1.088
r_mcbond_other1.087
r_angle_other_deg0.752
r_chiral_restr0.1
r_bond_refined_d0.012
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.001
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 Atoms1921
Nucleic Acid Atoms
Solvent Atoms340
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing