3I14

Cobalt-substituted metallo-beta-lactamase from Bacillus cereus: residue Cys168 partially oxidized


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.82930.1 M Sodium cacodylate, 0.1 M Sodium tartrate, 18% PEG 3350, 1 mM CoSO4, 1 mM DTT, pH 5.8, Vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2745.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.078α = 90
b = 61.699β = 93.09
c = 69.63γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2007-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.55340.22695.40.0280.02815.408631080
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.6387.20.1560.1564.55.34122

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.5535.4431080156995.850.1580.1570.191RANDOM16.118
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]
-0.13-0.630.86-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.993
r_dihedral_angle_4_deg15.309
r_sphericity_free15.019
r_dihedral_angle_3_deg12.59
r_dihedral_angle_1_deg6.849
r_sphericity_bonded6.788
r_scangle_it4.303
r_rigid_bond_restr3.094
r_scbond_it2.76
r_angle_refined_deg1.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.993
r_dihedral_angle_4_deg15.309
r_sphericity_free15.019
r_dihedral_angle_3_deg12.59
r_dihedral_angle_1_deg6.849
r_sphericity_bonded6.788
r_scangle_it4.303
r_rigid_bond_restr3.094
r_scbond_it2.76
r_angle_refined_deg1.95
r_mcangle_it1.904
r_mcbond_it1.175
r_angle_other_deg1.088
r_mcbond_other0.364
r_chiral_restr0.123
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1661
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms8

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction