3F9O

Crystal Structure of the Di-Zinc Carbapenemase CphA from Aeromonas Hydrophila


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62772.4M (NH4)2SO4, 100mM MES, 100mM ZnCl2, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.550.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.8α = 90
b = 101.05β = 90
c = 116.49γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirror2007-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.5418

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
12.0319.7199.70.06234.414167731675415.64
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)
12.032.1498.50.16117.613.32365

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRTHROUGHOUTPDB ENTRY 1X8G2.0314.56167731586384599.730.158860.158860.156680.20203RANDOM9.812
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]
0.03-0.050.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.766
r_dihedral_angle_4_deg15.725
r_dihedral_angle_3_deg12.973
r_dihedral_angle_1_deg6.199
r_scangle_it2.142
r_scbond_it1.561
r_angle_refined_deg1.217
r_angle_other_deg0.836
r_mcangle_it0.694
r_mcbond_it0.408
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.766
r_dihedral_angle_4_deg15.725
r_dihedral_angle_3_deg12.973
r_dihedral_angle_1_deg6.199
r_scangle_it2.142
r_scbond_it1.561
r_angle_refined_deg1.217
r_angle_other_deg0.836
r_mcangle_it0.694
r_mcbond_it0.408
r_mcbond_other0.106
r_chiral_restr0.072
r_bond_refined_d0.011
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1763
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms37

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling