3T9M

Crystal structure of 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, 100 nM zinc chloride, 1 mM EDTA, pH 4.6, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1843.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.605α = 90
b = 64.639β = 90
c = 67.14γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMIRRORS2009-05-26MSINGLE 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
12.0319.2997.50.05216.73.21434121.5
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)
12.032.1498.20.254.93.1

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 1X8G2.0319.29148041405275299.50.1810.1790.223RANDOM33.014
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]
5.28-1.56-3.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.794
r_dihedral_angle_3_deg13.21
r_dihedral_angle_4_deg12.846
r_dihedral_angle_1_deg6.283
r_scangle_it2.038
r_scbond_it1.272
r_angle_refined_deg1.217
r_angle_other_deg0.855
r_mcangle_it0.758
r_mcbond_it0.446
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.794
r_dihedral_angle_3_deg13.21
r_dihedral_angle_4_deg12.846
r_dihedral_angle_1_deg6.283
r_scangle_it2.038
r_scbond_it1.272
r_angle_refined_deg1.217
r_angle_other_deg0.855
r_mcangle_it0.758
r_mcbond_it0.446
r_mcbond_other0.122
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms1618
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms8

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling