4KQO

Crystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa in complex with piperacillin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OCLPDB ENTRY 3OCL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82932.5 M NaCl; 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7354.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.049α = 71.26
b = 74.935β = 86.04
c = 82.785γ = 85.59
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2011-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91730DiamondI04-1

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
12.315097.80.18569.455461-1.5
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)
12.312.3987.20.2751.55.94929

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 3OCL2.3147.152657280497.810.21880.217140.24965RANDOM42.412
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]
1.070.930.851.262.32-1.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.167
r_dihedral_angle_3_deg14.911
r_dihedral_angle_4_deg14.505
r_dihedral_angle_1_deg5.685
r_angle_refined_deg1.271
r_angle_other_deg0.861
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.167
r_dihedral_angle_3_deg14.911
r_dihedral_angle_4_deg14.505
r_dihedral_angle_1_deg5.685
r_angle_refined_deg1.271
r_angle_other_deg0.861
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7635
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms97

Software

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