2ZQC

Aztreonam acyl-intermediate structure of class a beta-lactam 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
2.6152.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.293α = 90
b = 72.293β = 90
c = 97.578γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2008-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B20.7SPring-8BL26B2

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
11.075099.90.07719.110.4129890
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)
11.071.0998.30.3135.167.3

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 2ZQ71.0750123290653999.850.134240.133590.14643RANDOM9.935
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]
0.020.010.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.562
r_dihedral_angle_3_deg10.801
r_dihedral_angle_4_deg10.134
r_dihedral_angle_1_deg6.305
r_sphericity_free4.599
r_sphericity_bonded3.693
r_scangle_it2.975
r_scbond_it2.109
r_mcangle_it1.583
r_angle_refined_deg1.496
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.562
r_dihedral_angle_3_deg10.801
r_dihedral_angle_4_deg10.134
r_dihedral_angle_1_deg6.305
r_sphericity_free4.599
r_sphericity_bonded3.693
r_scangle_it2.975
r_scbond_it2.109
r_mcangle_it1.583
r_angle_refined_deg1.496
r_mcbond_it1.072
r_rigid_bond_restr1.037
r_nbtor_refined0.306
r_nbd_refined0.197
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.123
r_symmetry_hbond_refined0.108
r_chiral_restr0.085
r_bond_refined_d0.009
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 Atoms1966
Nucleic Acid Atoms
Solvent Atoms410
Heterogen Atoms48

Software

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