5EPH

Crystal structure of extended-spectrum beta-lactamase BEL-1 in complex with Imipenem


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5EOE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.629820% PEG4600, 20% MPD, 0.1M sodium citrate, pH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.141.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.98α = 90
b = 95.86β = 91.97
c = 103.42γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

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
11.7951.6893.20.0847.52.491836216.443
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)
11.791.8996.40.3882.72.4

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 REPLACEMENTTHROUGHOUT5EOE1.7951.6887230457992.720.165450.16350.20239RANDOM20.741
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.848
r_dihedral_angle_4_deg19.37
r_dihedral_angle_3_deg12.442
r_dihedral_angle_1_deg6.11
r_long_range_B_refined4.932
r_long_range_B_other4.932
r_scangle_other3.323
r_mcangle_it2.319
r_mcangle_other2.319
r_scbond_it2.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.848
r_dihedral_angle_4_deg19.37
r_dihedral_angle_3_deg12.442
r_dihedral_angle_1_deg6.11
r_long_range_B_refined4.932
r_long_range_B_other4.932
r_scangle_other3.323
r_mcangle_it2.319
r_mcangle_other2.319
r_scbond_it2.212
r_scbond_other2.212
r_angle_refined_deg1.767
r_mcbond_it1.653
r_mcbond_other1.652
r_angle_other_deg0.961
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_bond_other_d0.004
r_gen_planes_other0.001
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 Atoms7862
Nucleic Acid Atoms
Solvent Atoms685
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPmodel building
SCALAdata scaling
iMOSFLMdata reduction