3M6H

Crystal Structure of Post-isomerized Ertapenem 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
2.2545.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.934α = 90
b = 67.83β = 90
c = 75.201γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2007-08-08MSINGLE 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
11.9945099.50.1919.84.41801017920
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)
11.9942.0799.90.42444.41762

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 3DWZ1.99430.041787891199.380.1770.1750.222RANDOM6.842
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]
0.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.601
r_dihedral_angle_4_deg21.6
r_dihedral_angle_3_deg10.984
r_dihedral_angle_1_deg6.058
r_scangle_it2.67
r_scbond_it1.769
r_angle_refined_deg1.386
r_mcangle_it0.963
r_mcbond_it0.637
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.601
r_dihedral_angle_4_deg21.6
r_dihedral_angle_3_deg10.984
r_dihedral_angle_1_deg6.058
r_scangle_it2.67
r_scbond_it1.769
r_angle_refined_deg1.386
r_mcangle_it0.963
r_mcbond_it0.637
r_nbtor_refined0.299
r_symmetry_vdw_refined0.214
r_nbd_refined0.211
r_xyhbond_nbd_refined0.136
r_symmetry_hbond_refined0.135
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1988
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms43

Software

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