5DF9

CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 IN COMPLEX WITH DEACYLATED PRODUCT OF CEFOPERAZONE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DF8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.52941.26 M (NH4)2SO4; 0.1 M CHES pH 9.5; 0.2 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.3347.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 176.884α = 90
b = 41.264β = 117.42
c = 87.786γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-01-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97960DiamondI02

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
12.7301000.09214.53.715866
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)
12.72.81000.7221.93.7

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 REPLACEMENTTHROUGHOUT5DF82.729.971502978699.580.20460.202360.24927RANDOM75.155
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]
-4.431.75-3.264.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.469
r_dihedral_angle_3_deg12.857
r_dihedral_angle_4_deg11.152
r_long_range_B_refined8.339
r_long_range_B_other8.337
r_scangle_other5.892
r_dihedral_angle_1_deg4.858
r_mcangle_it4.667
r_mcangle_other4.667
r_scbond_it3.664
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.469
r_dihedral_angle_3_deg12.857
r_dihedral_angle_4_deg11.152
r_long_range_B_refined8.339
r_long_range_B_other8.337
r_scangle_other5.892
r_dihedral_angle_1_deg4.858
r_mcangle_it4.667
r_mcangle_other4.667
r_scbond_it3.664
r_scbond_other3.662
r_mcbond_it2.987
r_mcbond_other2.978
r_angle_refined_deg0.903
r_angle_other_deg0.669
r_chiral_restr0.049
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3886
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms54

Software

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