3M6B

Crystal Structure of the Ertapenem Pre-isomerized Covalent Adduct with TB B-lactamase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DWZpdb entry 3DWZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop4.12980.1 M HEPES, 2 M NH4(H2)PO4, pH 4.1, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2545.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.657α = 90
b = 67.922β = 90
c = 75.546γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-01-21MSINGLE 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
11.3501000.05721.47.56348563485
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)
11.31.331000.7571.85.74388

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 3DWZ1.326.2860263322299.960.1490.1470.176RANDOM13.287
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]
0.03-0.040.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.298
r_dihedral_angle_4_deg21.341
r_dihedral_angle_3_deg11.508
r_dihedral_angle_1_deg6.091
r_scangle_it4.451
r_scbond_it3.009
r_mcangle_it1.959
r_angle_refined_deg1.428
r_rigid_bond_restr1.292
r_mcbond_it1.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.298
r_dihedral_angle_4_deg21.341
r_dihedral_angle_3_deg11.508
r_dihedral_angle_1_deg6.091
r_scangle_it4.451
r_scbond_it3.009
r_mcangle_it1.959
r_angle_refined_deg1.428
r_rigid_bond_restr1.292
r_mcbond_it1.198
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1988
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling