5EUA

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


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
2.244.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.53α = 90
b = 80.91β = 90
c = 86.64γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2013-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.920DiamondI04-1

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
11.8533.5899.70.0812.66.242901219.68
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)
11.851.951000.4273.86.5

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 REPLACEMENTTHROUGHOUT5EOE1.8533.5840684215999.60.1680.1660.215RANDOM27.59
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.066
r_dihedral_angle_4_deg16.674
r_dihedral_angle_3_deg12.956
r_dihedral_angle_1_deg6.111
r_long_range_B_other5.668
r_long_range_B_refined5.666
r_scangle_other3.93
r_mcangle_other3.025
r_mcangle_it3.024
r_scbond_it2.616
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.066
r_dihedral_angle_4_deg16.674
r_dihedral_angle_3_deg12.956
r_dihedral_angle_1_deg6.111
r_long_range_B_other5.668
r_long_range_B_refined5.666
r_scangle_other3.93
r_mcangle_other3.025
r_mcangle_it3.024
r_scbond_it2.616
r_scbond_other2.615
r_mcbond_it2.156
r_mcbond_other2.152
r_angle_refined_deg1.697
r_angle_other_deg0.877
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
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 Atoms3888
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALAdata scaling
iMOSFLMdata reduction