8IXX

Crystal structure of Class A beta-lactamase BlaA WT - complex with Ertapenem


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5E2E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic
Crystal Properties
Matthews coefficientSolvent content
2.2946.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.743α = 90
b = 72.818β = 95.776
c = 43.7γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HEX ray optics2022-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.724.66399.80.1290.1520.0780.9897.46.531443
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.730.5230.6740.4180.8094

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.724.66331440160899.7910.1870.1850.218518.766
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]
2.0380.47-1.071-1.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.411
r_dihedral_angle_6_deg15.575
r_dihedral_angle_3_deg13.595
r_dihedral_angle_1_deg6.731
r_lrange_it6.315
r_lrange_other5.81
r_scangle_it4.247
r_scangle_other4.14
r_scbond_it2.807
r_scbond_other2.709
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.411
r_dihedral_angle_6_deg15.575
r_dihedral_angle_3_deg13.595
r_dihedral_angle_1_deg6.731
r_lrange_it6.315
r_lrange_other5.81
r_scangle_it4.247
r_scangle_other4.14
r_scbond_it2.807
r_scbond_other2.709
r_mcangle_it2.363
r_mcangle_other2.361
r_mcbond_it1.669
r_mcbond_other1.668
r_angle_refined_deg1.638
r_angle_other_deg0.533
r_xyhbond_nbd_refined0.226
r_nbd_refined0.22
r_symmetry_nbd_other0.191
r_symmetry_xyhbond_nbd_refined0.183
r_nbtor_refined0.181
r_symmetry_nbd_refined0.171
r_nbd_other0.17
r_chiral_restr0.082
r_symmetry_nbtor_other0.082
r_chiral_restr_other0.02
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_symmetry_xyhbond_nbd_other0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2004
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
Cootmodel building
CrysalisProdata collection
MOLREPphasing