4JXW

X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with a non-covalent inhibitor 3-{[3-(4-CARBOXYPHENYL)PROPYL]SULFAMOYL}THIOPHENE-2-CARBOXYLIC ACID (compound 6)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.72961.7 M potassium phosphate, 3.5 mg/mL AmpC , pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.5952.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.914α = 90
b = 77.736β = 115.36
c = 98.354γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2007-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.0APS21-ID-D

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
12.35094.70.06716.63426234262
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)
12.32.3899.20.366

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.35032548169694.690.185260.181620.25667RANDOM45.98
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]
0.690.33-0.760.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.965
r_dihedral_angle_4_deg19.702
r_dihedral_angle_3_deg15.091
r_dihedral_angle_1_deg7.605
r_scangle_it4.195
r_scbond_it2.966
r_angle_refined_deg2.072
r_mcangle_it1.674
r_mcbond_it1.098
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.965
r_dihedral_angle_4_deg19.702
r_dihedral_angle_3_deg15.091
r_dihedral_angle_1_deg7.605
r_scangle_it4.195
r_scbond_it2.966
r_angle_refined_deg2.072
r_mcangle_it1.674
r_mcbond_it1.098
r_nbtor_refined0.315
r_nbd_refined0.223
r_symmetry_hbond_refined0.222
r_symmetry_vdw_refined0.22
r_xyhbond_nbd_refined0.18
r_chiral_restr0.141
r_bond_refined_d0.026
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5479
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms53

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling