4GZB

Crystal structure of native AmpC beta-lactamase from Pseudomonas aeruginosa PAO1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KE4PDB ENTRY 1KE4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1M Tris, 20% PEG 8000, O.1M K2HPO4, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9958.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.06α = 90
b = 83.06β = 90
c = 122.42γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9360ESRFID29

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
11.7946.61783.30.0628.72.1383173831726.695
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)
11.791.8982.70.3741.81.89784

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 1KE41.7934.5136340197582.070.192960.190160.24384RANDOM28.534
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.11
r_dihedral_angle_3_deg15.577
r_dihedral_angle_4_deg14.2
r_dihedral_angle_1_deg6.697
r_scangle_it5.358
r_scbond_it3.483
r_angle_refined_deg2.029
r_mcangle_it1.951
r_mcbond_it1.207
r_chiral_restr0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.11
r_dihedral_angle_3_deg15.577
r_dihedral_angle_4_deg14.2
r_dihedral_angle_1_deg6.697
r_scangle_it5.358
r_scbond_it3.483
r_angle_refined_deg2.029
r_mcangle_it1.951
r_mcbond_it1.207
r_chiral_restr0.18
r_bond_refined_d0.023
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2839
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms4

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling