2ZQ8

Apo structure of class a beta-lactamase Toho-1 R274N/R276N double 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
2.6253.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.511α = 90
b = 72.511β = 90
c = 97.477γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS Vmirrors2007-11-21MSINGLE 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
11.03501000.07227.179.9146345
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)
1.031.0599.90.3567.339

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 2ZQ71.0350138865732399.930.138140.137630.1481RANDOM11.223
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]
-0.19-0.09-0.190.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.436
r_dihedral_angle_3_deg11.132
r_dihedral_angle_4_deg9.229
r_dihedral_angle_1_deg6.247
r_sphericity_free4.597
r_sphericity_bonded4.228
r_scangle_it3.096
r_scbond_it2.221
r_mcangle_it1.74
r_angle_refined_deg1.415
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.436
r_dihedral_angle_3_deg11.132
r_dihedral_angle_4_deg9.229
r_dihedral_angle_1_deg6.247
r_sphericity_free4.597
r_sphericity_bonded4.228
r_scangle_it3.096
r_scbond_it2.221
r_mcangle_it1.74
r_angle_refined_deg1.415
r_mcbond_it1.183
r_rigid_bond_restr1.075
r_nbtor_refined0.307
r_nbd_refined0.204
r_symmetry_vdw_refined0.163
r_xyhbond_nbd_refined0.13
r_symmetry_hbond_refined0.109
r_chiral_restr0.093
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 Atoms2248
Nucleic Acid Atoms
Solvent Atoms455
Heterogen Atoms30

Software

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