3SW3

EDTA-free crystal structure of the mutant C221D of carbapenemase CphA from Aeromonas hydrophila


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.62770.05 M sodium acetate, 0.05 M potassium phosphate monobasic, 20% PEG8000, 2 mM zinc chloride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2445.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.622α = 90
b = 65.021β = 90
c = 67.272γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMIRROR2009-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR591

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.3519.6199.60.06916.34.3984533.33
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.4898.60.2645.24.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1X8G2.3519.6198029323469990.1920.1890.261RANDOM42.695
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]
3.62-0.47-3.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.273
r_dihedral_angle_4_deg21.951
r_dihedral_angle_3_deg15.242
r_dihedral_angle_1_deg7.141
r_scangle_it3.217
r_scbond_it2.141
r_angle_refined_deg1.707
r_mcangle_it1.27
r_angle_other_deg1.043
r_mcbond_it0.746
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.273
r_dihedral_angle_4_deg21.951
r_dihedral_angle_3_deg15.242
r_dihedral_angle_1_deg7.141
r_scangle_it3.217
r_scbond_it2.141
r_angle_refined_deg1.707
r_mcangle_it1.27
r_angle_other_deg1.043
r_mcbond_it0.746
r_mcbond_other0.209
r_chiral_restr0.102
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.001
r_bond_other_d
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1613
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling