3MZE

Structure of penicillin-binding protein 5 from E.coli: cefoxitin acyl-enzyme complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NZOPDB entry 1NZO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7294100 MM TRIS PH 7.0, 8 % PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.5151

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.42α = 90
b = 50.34β = 120.44
c = 84.23γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++osmic blue2001-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.1541000.0950.0955.24.3233072330731.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.181000.3710.3711.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1NZO2.1542324123241119799.720.2280.2280.2250.281RANDOM28.57
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]
0.34-0.1-0.930.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.656
r_dihedral_angle_3_deg16.321
r_dihedral_angle_4_deg15.507
r_dihedral_angle_1_deg6.608
r_scangle_it2.564
r_scbond_it1.63
r_angle_refined_deg1.493
r_mcangle_it1.167
r_mcbond_it0.68
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.656
r_dihedral_angle_3_deg16.321
r_dihedral_angle_4_deg15.507
r_dihedral_angle_1_deg6.608
r_scangle_it2.564
r_scbond_it1.63
r_angle_refined_deg1.493
r_mcangle_it1.167
r_mcbond_it0.68
r_nbtor_refined0.294
r_nbd_refined0.205
r_symmetry_hbond_refined0.173
r_symmetry_vdw_refined0.167
r_xyhbond_nbd_refined0.153
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2713
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing