5B1U

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG5000, Lithium sulfate, Tris-Hydrochloride
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.03α = 108.32
b = 41.46β = 102.78
c = 45.44γ = 106.28
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702015-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.00Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.5740.5893.6193.330412
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)
11.571.6592.70.07911.93.4

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 REPLACEMENTTHROUGHOUT3VPE1.5740.5828877153493.630.124060.122410.15472RANDOM7.866
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]
0.20.29-0.230.49-0.28-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.565
r_dihedral_angle_4_deg19.656
r_dihedral_angle_3_deg12.196
r_dihedral_angle_1_deg6.869
r_long_range_B_refined5.459
r_long_range_B_other5.109
r_scangle_other3.088
r_scbond_it2.079
r_scbond_other2.078
r_angle_refined_deg1.433
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.565
r_dihedral_angle_4_deg19.656
r_dihedral_angle_3_deg12.196
r_dihedral_angle_1_deg6.869
r_long_range_B_refined5.459
r_long_range_B_other5.109
r_scangle_other3.088
r_scbond_it2.079
r_scbond_other2.078
r_angle_refined_deg1.433
r_mcangle_other1.268
r_mcangle_it1.267
r_mcbond_it0.819
r_mcbond_other0.814
r_angle_other_deg0.74
r_chiral_restr0.096
r_gen_planes_refined0.013
r_bond_refined_d0.011
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 Atoms378
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing