6H2G

Structure of BlaC from Mycobacterium tuberculosis bound to the propionaldehyde ester adduct of clavulanic acid.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.50.1 M sodium acetate buffer, pH 5.0 25% w/v PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.0439.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.398α = 75.67
b = 41.314β = 89.96
c = 76.222γ = 89.26
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9763ESRFID29

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
12.840.0379.20.10.98451.69073
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)
12.82.9580.90.2430.8812.11.6

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 REPLACEMENTTHROUGHOUT2GDN2.840.03862144979.120.21590.212280.28908RANDOM28.119
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]
-5.291.19-1.174.6-2.16-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.795
r_dihedral_angle_4_deg18.65
r_dihedral_angle_3_deg16.922
r_dihedral_angle_1_deg6.808
r_long_range_B_refined4.217
r_long_range_B_other4.216
r_mcangle_other2.402
r_mcangle_it2.4
r_scangle_other2.018
r_angle_refined_deg1.481
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.795
r_dihedral_angle_4_deg18.65
r_dihedral_angle_3_deg16.922
r_dihedral_angle_1_deg6.808
r_long_range_B_refined4.217
r_long_range_B_other4.216
r_mcangle_other2.402
r_mcangle_it2.4
r_scangle_other2.018
r_angle_refined_deg1.481
r_mcbond_it1.452
r_mcbond_other1.446
r_scbond_it1.18
r_scbond_other1.18
r_angle_other_deg0.994
r_chiral_restr0.072
r_bond_refined_d0.012
r_gen_planes_refined0.005
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 Atoms4036
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing