3A3F

Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae,complexed with novel beta-lactam (FMZ)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M HEPES pH 7.5, 25% (w/v) PEG 6000 and 5% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9858.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.799α = 90
b = 92.103β = 107.95
c = 104.454γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.0Photon FactoryBL-17A

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
12.120960.0553.465444
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)
12.12.17850.197

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 REPLACEMENTTHROUGHOUT2.119.876211233171000.19210.189740.23559RANDOM30.766
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]
-0.01-0.060.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.023
r_dihedral_angle_4_deg21.439
r_dihedral_angle_3_deg16.299
r_dihedral_angle_1_deg6.457
r_scangle_it5.327
r_scbond_it3.467
r_mcangle_it2.129
r_angle_refined_deg2.088
r_mcbond_it1.219
r_chiral_restr0.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.023
r_dihedral_angle_4_deg21.439
r_dihedral_angle_3_deg16.299
r_dihedral_angle_1_deg6.457
r_scangle_it5.327
r_scbond_it3.467
r_mcangle_it2.129
r_angle_refined_deg2.088
r_mcbond_it1.219
r_chiral_restr0.139
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms7006
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms60

Software

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