2ZQ7

Apo structure of Class A beta-lactamase Toho-1 E166A/R274N/R276N triple mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IYOPDB ENTRY 1IYO

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
2.6353.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.545α = 90
b = 72.545β = 90
c = 97.656γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS Vmirrors2007-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B10.8SPring-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
10.945099.90.07525.9910.1192768
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)
0.940.9698.90.3844.325.7

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 1IYO0.9450182648967099.920.13580.135190.14726RANDOM10.475
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]
-0.23-0.12-0.230.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.841
r_dihedral_angle_4_deg13.007
r_dihedral_angle_3_deg10.695
r_dihedral_angle_1_deg6.354
r_sphericity_free5.02
r_sphericity_bonded4.634
r_scangle_it3.159
r_scbond_it2.314
r_mcangle_it1.847
r_angle_refined_deg1.495
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.841
r_dihedral_angle_4_deg13.007
r_dihedral_angle_3_deg10.695
r_dihedral_angle_1_deg6.354
r_sphericity_free5.02
r_sphericity_bonded4.634
r_scangle_it3.159
r_scbond_it2.314
r_mcangle_it1.847
r_angle_refined_deg1.495
r_mcbond_it1.285
r_rigid_bond_restr1.049
r_nbtor_refined0.307
r_nbd_refined0.207
r_symmetry_vdw_refined0.176
r_xyhbond_nbd_refined0.115
r_symmetry_hbond_refined0.109
r_chiral_restr0.093
r_bond_refined_d0.01
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2267
Nucleic Acid Atoms
Solvent Atoms511
Heterogen Atoms30

Software

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