3MZF

Structure of penicillin-binding protein 5 from E. coli: imipenem acyl-enzyme complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NZOPDB entry 1NZO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7294100 MM TRIS PH 7.0, 8 % PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.5351.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.78α = 90
b = 50.35β = 120.16
c = 84.29γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2004-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.53396.60.0550.05540.16.8618866188620.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5576.30.4880.4881.83.94880

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1NZO1.532.976182361823312396.70.1890.1890.1880.212RANDOM22.92
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]
-0.16-0.41-0.560.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.07
r_dihedral_angle_4_deg18.226
r_dihedral_angle_3_deg11.55
r_dihedral_angle_1_deg5.506
r_rigid_bond_restr5.095
r_scbond_it4.443
r_scangle_it3.948
r_sphericity_free3.375
r_sphericity_bonded3.37
r_mcangle_it1.496
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.07
r_dihedral_angle_4_deg18.226
r_dihedral_angle_3_deg11.55
r_dihedral_angle_1_deg5.506
r_rigid_bond_restr5.095
r_scbond_it4.443
r_scangle_it3.948
r_sphericity_free3.375
r_sphericity_bonded3.37
r_mcangle_it1.496
r_angle_refined_deg1.225
r_mcbond_it1.021
r_nbtor_refined0.301
r_nbd_refined0.193
r_symmetry_vdw_refined0.115
r_xyhbond_nbd_refined0.105
r_symmetry_hbond_refined0.09
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2740
Nucleic Acid Atoms
Solvent Atoms369
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing