2EX6

Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with ampicillin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52935% PEG 20000, 0.1M MES(pH6.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6653.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.704α = 90
b = 95.704β = 90
c = 115.952γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.00000Photon FactoryBL-5A

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
11.65095.20.0614.96.868074
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)
11.61.6669.90.311

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 REPLACEMENTTHROUGHOUT1.6206457934491000.217790.21610.24977RANDOM34.02
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]
-0.1-0.10.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.504
r_dihedral_angle_4_deg21.208
r_dihedral_angle_3_deg14.899
r_dihedral_angle_1_deg5.988
r_scangle_it3.536
r_scbond_it2.515
r_mcangle_it1.492
r_angle_refined_deg1.458
r_mcbond_it0.985
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.504
r_dihedral_angle_4_deg21.208
r_dihedral_angle_3_deg14.899
r_dihedral_angle_1_deg5.988
r_scangle_it3.536
r_scbond_it2.515
r_mcangle_it1.492
r_angle_refined_deg1.458
r_mcbond_it0.985
r_nbtor_refined0.309
r_nbd_refined0.211
r_symmetry_vdw_refined0.167
r_symmetry_hbond_refined0.158
r_xyhbond_nbd_refined0.113
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.006
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 Atoms3433
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing