3CG5

Crystal Structure of the Covalent Adduct Formed between TB B-lactamase and Clavulanate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GDNPDB entry 2GDN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.12980.1 M HEPES pH 7.5, 2 M NH4(H2)PO4, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2344.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.666α = 90
b = 67.655β = 90
c = 75.032γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.100NSLSX12C

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
11.741.4960.05183.3273492734915.76
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)
1.71.74880.4231732

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 REPLACEMENTTHROUGHOUTPDB entry 2GDN1.741.425961138895.990.181390.179740.21177RANDOM13.99
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.358
r_dihedral_angle_4_deg21.684
r_dihedral_angle_3_deg11.729
r_dihedral_angle_1_deg11.074
r_scangle_it3.113
r_scbond_it2.046
r_angle_refined_deg1.508
r_mcangle_it1.094
r_mcbond_it0.732
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.358
r_dihedral_angle_4_deg21.684
r_dihedral_angle_3_deg11.729
r_dihedral_angle_1_deg11.074
r_scangle_it3.113
r_scbond_it2.046
r_angle_refined_deg1.508
r_mcangle_it1.094
r_mcbond_it0.732
r_nbtor_refined0.302
r_nbd_refined0.23
r_symmetry_vdw_refined0.217
r_symmetry_hbond_refined0.145
r_xyhbond_nbd_refined0.134
r_chiral_restr0.102
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1988
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing