3MZD

Structure of penicillin-binding protein 5 from E. coli: cloxacillin 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
2.5251.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.84α = 90
b = 50.23β = 119.93
c = 84.03γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++OSMIC BLUE2001-12-07MSINGLE 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
11.95497.50.0730.07374.9307373073726
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)
11.91.9778.50.3360.33623.63096

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 1NZO1.9543068030680155597.30.2160.2160.2140.257RANDOM25.779
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]
-0.22-0.39-0.70.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.9
r_dihedral_angle_3_deg14.901
r_dihedral_angle_4_deg14.203
r_dihedral_angle_1_deg6.005
r_scangle_it2.365
r_scbond_it1.534
r_angle_refined_deg1.374
r_mcangle_it1.162
r_mcbond_it0.706
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.9
r_dihedral_angle_3_deg14.901
r_dihedral_angle_4_deg14.203
r_dihedral_angle_1_deg6.005
r_scangle_it2.365
r_scbond_it1.534
r_angle_refined_deg1.374
r_mcangle_it1.162
r_mcbond_it0.706
r_nbtor_refined0.294
r_nbd_refined0.19
r_symmetry_vdw_refined0.147
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.142
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2732
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms35

Software

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