4YFM

Class A beta-lactamase from Mycobacterium abscessus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1 M sodium acetate, 0.1 MES (pH 6.5), 32% polyethylene glycol monomethyl ether 2000
Crystal Properties
Matthews coefficientSolvent content
2.1241.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.49α = 90
b = 65.21β = 90.94
c = 107.42γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9801SOLEILPROXIMA 1

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
11.441.594.60.06611.293.393890
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)
11.41.4873.20.6691.342

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 REPLACEMENTTHROUGHOUT2GDN1.441.4589195469594.60.144470.143070.1712RANDOM18.543
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]
-0.960.68-0.361.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.002
r_dihedral_angle_4_deg17.086
r_dihedral_angle_3_deg11.295
r_long_range_B_refined6.189
r_long_range_B_other5.95
r_dihedral_angle_1_deg5.602
r_scangle_other4.85
r_scbond_it3.32
r_scbond_other3.309
r_mcangle_it2.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.002
r_dihedral_angle_4_deg17.086
r_dihedral_angle_3_deg11.295
r_long_range_B_refined6.189
r_long_range_B_other5.95
r_dihedral_angle_1_deg5.602
r_scangle_other4.85
r_scbond_it3.32
r_scbond_other3.309
r_mcangle_it2.123
r_mcangle_other2.123
r_angle_refined_deg2.027
r_mcbond_it1.617
r_mcbond_other1.496
r_angle_other_deg0.948
r_chiral_restr0.133
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3952
Nucleic Acid Atoms
Solvent Atoms469
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing