5NGG

Crystal structure of the subclass B3 metallo-beta-lactamase BJP-1 in complex with acetate anion


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5295BJP-1 (10 mg mL-1 in 0.1 M Tris-HCl pH 8.5 and 5 mM zinc(II) chloride) mixed with precipitant (0.2 M lithium sulfate, 30-35 % PEG4000, 0.5 M sodium acetate pH 8.5)
Crystal Properties
Matthews coefficientSolvent content
1.9336.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.31α = 78.88
b = 44.64β = 89.41
c = 75.91γ = 61.99
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.1834.6894.50.060.9979.8414895926.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.181.2492.20.3870.80634

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 REPLACEMENTTHROUGHOUT3LVZ1.1834.68141256770394.50.1220.120710.14601RANDOM14.912
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]
-0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.073
r_sphericity_free24.653
r_dihedral_angle_4_deg20.02
r_sphericity_bonded11.876
r_dihedral_angle_3_deg11.437
r_dihedral_angle_1_deg5.716
r_rigid_bond_restr3.428
r_long_range_B_refined3.06
r_long_range_B_other2.714
r_scangle_other2.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.073
r_sphericity_free24.653
r_dihedral_angle_4_deg20.02
r_sphericity_bonded11.876
r_dihedral_angle_3_deg11.437
r_dihedral_angle_1_deg5.716
r_rigid_bond_restr3.428
r_long_range_B_refined3.06
r_long_range_B_other2.714
r_scangle_other2.154
r_angle_other_deg2.067
r_mcangle_other1.719
r_mcangle_it1.718
r_scbond_it1.62
r_scbond_other1.62
r_mcbond_it1.487
r_mcbond_other1.484
r_angle_refined_deg1.458
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.006
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4100
Nucleic Acid Atoms
Solvent Atoms627
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing