2ZQD

Ceftazidime acyl-intermediate structure of class a beta-lact Toho-1 E166A/R274N/R276N triple mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZQ7PDB ENTRY 2ZQ7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52981.95-2.10M Ammonium sulfate, 0.2M sodium citrate, PH5.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6153.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.413α = 90
b = 72.413β = 90
c = 97.665γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210mirrors2008-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B10.7SPring-8BL26B1

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
11.19501000.05642.9710.495363
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)
1.191.2199.80.3755.027.8

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 2ZQ71.195090431477799.970.139720.138690.1587RANDOM12.746
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]
-0.08-0.04-0.080.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.78
r_dihedral_angle_3_deg10.615
r_dihedral_angle_4_deg10.128
r_dihedral_angle_1_deg6.301
r_sphericity_free6.002
r_sphericity_bonded4.39
r_scangle_it3.6
r_scbond_it2.823
r_rigid_bond_restr1.943
r_mcangle_it1.827
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.78
r_dihedral_angle_3_deg10.615
r_dihedral_angle_4_deg10.128
r_dihedral_angle_1_deg6.301
r_sphericity_free6.002
r_sphericity_bonded4.39
r_scangle_it3.6
r_scbond_it2.823
r_rigid_bond_restr1.943
r_mcangle_it1.827
r_angle_refined_deg1.494
r_mcbond_it1.26
r_nbtor_refined0.308
r_nbd_refined0.208
r_symmetry_vdw_refined0.162
r_xyhbond_nbd_refined0.134
r_symmetry_hbond_refined0.132
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.008
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2181
Nucleic Acid Atoms
Solvent Atoms394
Heterogen Atoms51

Software

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