2JCH

Structural and mechanistic basis of penicillin binding protein inhibition by lactivicins


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BG1PDB ENTRY 2BG1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1750 MM HEPES PH 7 3.2 M NACL 0.8 M AMMONIUM SULFATE
Crystal Properties
Matthews coefficientSolvent content
3.567.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.84α = 90
b = 143.58β = 90
c = 97.44γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.419.999.30.0912.95.2292943
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)
12.42.61000.432.94.7

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 2BG12.485.1327860143499.30.2060.2030.262RANDOM29.7
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]
1.79-0.04-1.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.168
r_dihedral_angle_3_deg20.094
r_dihedral_angle_4_deg19.537
r_dihedral_angle_1_deg8.299
r_scangle_it4.863
r_scbond_it3.347
r_angle_refined_deg2.398
r_mcangle_it2.18
r_mcbond_it1.321
r_symmetry_vdw_refined0.474
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.168
r_dihedral_angle_3_deg20.094
r_dihedral_angle_4_deg19.537
r_dihedral_angle_1_deg8.299
r_scangle_it4.863
r_scbond_it3.347
r_angle_refined_deg2.398
r_mcangle_it2.18
r_mcbond_it1.321
r_symmetry_vdw_refined0.474
r_symmetry_hbond_refined0.341
r_nbtor_refined0.312
r_nbd_refined0.247
r_xyhbond_nbd_refined0.2
r_chiral_restr0.156
r_bond_refined_d0.028
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3550
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing