6J25

CTX-M-64 beta-lactamase mutant-S130T


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2890.1M HEPES pH 7.4 25% PEG10000
Crystal Properties
Matthews coefficientSolvent content
1.8433.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.25α = 90
b = 105.99β = 100.73
c = 47.97γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2018-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.97917SSRFBL17U1

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
11.0453.2280.30.07113.86170268
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)
11.041.070.4071.6

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 REPLACEMENTTHROUGHOUT5twd1.252.99129002673698.230.182310.181690.19407RANDOM11.174
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.893
r_dihedral_angle_4_deg12.279
r_dihedral_angle_3_deg11.266
r_dihedral_angle_1_deg6.705
r_long_range_B_refined4.355
r_long_range_B_other4.093
r_scangle_other3.431
r_scbond_it2.427
r_scbond_other2.426
r_angle_refined_deg2.418
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.893
r_dihedral_angle_4_deg12.279
r_dihedral_angle_3_deg11.266
r_dihedral_angle_1_deg6.705
r_long_range_B_refined4.355
r_long_range_B_other4.093
r_scangle_other3.431
r_scbond_it2.427
r_scbond_other2.426
r_angle_refined_deg2.418
r_mcangle_other1.751
r_mcangle_it1.743
r_mcbond_it1.296
r_mcbond_other1.239
r_angle_other_deg1.2
r_chiral_restr0.169
r_bond_refined_d0.028
r_gen_planes_refined0.014
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3898
Nucleic Acid Atoms
Solvent Atoms614
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing