6H2C

Structure of BlaC from Mycobacterium tuberculosis bound to the trans-enamine adduct derived from clavulanic acid.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.150.1 M sodium acetate, pH 5.0 25% w/v PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.1342.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.65α = 78.4
b = 41.98β = 89.95
c = 76.917γ = 89.75
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2015-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9677ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.9341.1294.40.1240.9744.42.334426
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.93285.40.3420.7091.82.1

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 REPLACEMENTTHROUGHOUT2GDN1.9341.1232697172394.430.230540.228590.26694RANDOM14.358
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]
-0.950.26-0.352.730.37-1.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.399
r_dihedral_angle_4_deg20.152
r_dihedral_angle_3_deg14.555
r_dihedral_angle_1_deg6.185
r_long_range_B_refined2.903
r_long_range_B_other2.902
r_angle_refined_deg1.66
r_scangle_other1.602
r_mcangle_it1.443
r_mcangle_other1.442
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.399
r_dihedral_angle_4_deg20.152
r_dihedral_angle_3_deg14.555
r_dihedral_angle_1_deg6.185
r_long_range_B_refined2.903
r_long_range_B_other2.902
r_angle_refined_deg1.66
r_scangle_other1.602
r_mcangle_it1.443
r_mcangle_other1.442
r_scbond_it1.026
r_scbond_other1.026
r_angle_other_deg1.014
r_mcbond_it0.892
r_mcbond_other0.89
r_chiral_restr0.087
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4018
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing